Starting phenix.real_space_refine on Fri Mar 6 06:26:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pif_20349/03_2026/6pif_20349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pif_20349/03_2026/6pif_20349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pif_20349/03_2026/6pif_20349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pif_20349/03_2026/6pif_20349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pif_20349/03_2026/6pif_20349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pif_20349/03_2026/6pif_20349.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 142 5.16 5 C 18194 2.51 5 N 5003 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28954 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2742 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4093 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 495} Chain breaks: 1 Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2909 Classifications: {'peptide': 355} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 332} Chain breaks: 3 Chain: "J" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2982 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Time building chain proxies: 6.62, per 1000 atoms: 0.23 Number of scatterers: 28954 At special positions: 0 Unit cell: (133, 164.35, 184.3, 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 142 16.00 P 59 15.00 O 5556 8.00 N 5003 7.00 C 18194 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 38 sheets defined 26.0% alpha, 13.0% beta 6 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.535A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.591A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.903A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.661A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.946A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 4.007A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.873A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.675A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.973A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.712A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.569A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.634A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.776A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.932A pdb=" N SER C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.898A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.686A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.803A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.842A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.897A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.708A pdb=" N GLN D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 319 removed outlier: 3.670A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 344 removed outlier: 3.504A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.846A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.519A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.648A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.003A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 182' Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.906A pdb=" N ASN E 186 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP E 187 " --> pdb=" O ASN E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.600A pdb=" N ILE E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 320 " --> pdb=" O TYR E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 342 removed outlier: 3.700A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 Processing helix chain 'F' and resid 125 through 135 removed outlier: 4.068A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.913A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 264 through 269 removed outlier: 4.021A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.682A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 344 removed outlier: 3.852A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.050A pdb=" N PHE G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.516A pdb=" N VAL G 44 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 160 through 167 removed outlier: 3.501A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 Processing helix chain 'G' and resid 219 through 228 removed outlier: 3.733A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.538A pdb=" N MET G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.829A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 499 removed outlier: 3.684A pdb=" N VAL G 497 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 removed outlier: 3.713A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 558 removed outlier: 3.649A pdb=" N LEU G 553 " --> pdb=" O ASN G 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.822A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.693A pdb=" N LEU H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.242A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU I 35 " --> pdb=" O HIS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 82 removed outlier: 3.695A pdb=" N THR I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 218 through 228 removed outlier: 3.693A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET I 228 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 246 through 248 No H-bonds generated for 'chain 'I' and resid 246 through 248' Processing helix chain 'I' and resid 249 through 265 removed outlier: 3.969A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 4.250A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 303 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 Processing helix chain 'I' and resid 337 through 345 Processing helix chain 'I' and resid 369 through 379 Processing helix chain 'J' and resid 14 through 23 removed outlier: 3.628A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 43 Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.723A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.622A pdb=" N GLY J 206 " --> pdb=" O ASN J 202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS J 207 " --> pdb=" O TRP J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.607A pdb=" N ARG J 220 " --> pdb=" O PRO J 216 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.513A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE J 261 " --> pdb=" O ASP J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 310 removed outlier: 3.657A pdb=" N LEU J 303 " --> pdb=" O ILE J 299 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 310 " --> pdb=" O TYR J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 333 removed outlier: 3.739A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 345 Processing helix chain 'J' and resid 369 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.597A pdb=" N SER A 88 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 166 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 41 removed outlier: 3.500A pdb=" N VAL A 73 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 removed outlier: 4.081A pdb=" N GLU A 254 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 15 removed outlier: 3.733A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.830A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB3, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.795A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB6, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB7, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.781A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC3, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.891A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.394A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD1, first strand: chain 'G' and resid 201 through 204 removed outlier: 3.726A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.560A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD4, first strand: chain 'G' and resid 457 through 458 Processing sheet with id=AD5, first strand: chain 'G' and resid 539 through 542 Processing sheet with id=AD6, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.664A pdb=" N VAL H 90 " --> pdb=" O TYR H 5 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AD9, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.599A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.585A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 322 through 324 748 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5575 1.34 - 1.46: 7880 1.46 - 1.58: 16036 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29814 Sorted by residual: bond pdb=" CD GLU D 127 " pdb=" OE1 GLU D 127 " ideal model delta sigma weight residual 1.249 1.415 -0.166 1.90e-02 2.77e+03 7.61e+01 bond pdb=" CD GLU D 127 " pdb=" OE2 GLU D 127 " ideal model delta sigma weight residual 1.249 1.378 -0.129 1.90e-02 2.77e+03 4.62e+01 bond pdb=" N GLY D 285 " pdb=" CA GLY D 285 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta sigma weight residual 1.460 1.497 -0.037 8.60e-03 1.35e+04 1.81e+01 bond pdb=" N ILE J 347 " pdb=" CA ILE J 347 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.80e+01 ... (remaining 29809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 29066 1.84 - 3.69: 9943 3.69 - 5.53: 1612 5.53 - 7.37: 111 7.37 - 9.22: 10 Bond angle restraints: 40742 Sorted by residual: angle pdb=" N PRO I 86 " pdb=" CA PRO I 86 " pdb=" CB PRO I 86 " ideal model delta sigma weight residual 103.08 97.36 5.72 9.70e-01 1.06e+00 3.48e+01 angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 97.27 5.98 1.05e+00 9.07e-01 3.24e+01 angle pdb=" C CYS I 131 " pdb=" CA CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.08e+01 angle pdb=" CA GLY H 177 " pdb=" C GLY H 177 " pdb=" O GLY H 177 " ideal model delta sigma weight residual 122.33 117.88 4.45 8.10e-01 1.52e+00 3.02e+01 angle pdb=" N PRO D 276 " pdb=" CA PRO D 276 " pdb=" CB PRO D 276 " ideal model delta sigma weight residual 103.25 97.79 5.46 1.05e+00 9.07e-01 2.70e+01 ... (remaining 40737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17266 35.78 - 71.56: 509 71.56 - 107.34: 42 107.34 - 143.12: 4 143.12 - 178.90: 3 Dihedral angle restraints: 17824 sinusoidal: 7710 harmonic: 10114 Sorted by residual: dihedral pdb=" CA LYS G 49 " pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta harmonic sigma weight residual 180.00 45.09 134.91 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" CA LEU G 57 " pdb=" C LEU G 57 " pdb=" N ASP G 58 " pdb=" CA ASP G 58 " ideal model delta harmonic sigma weight residual 180.00 68.17 111.83 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA ASP G 58 " pdb=" C ASP G 58 " pdb=" N ARG G 59 " pdb=" CA ARG G 59 " ideal model delta harmonic sigma weight residual -180.00 -73.00 -107.00 0 5.00e+00 4.00e-02 4.58e+02 ... (remaining 17821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2064 0.057 - 0.115: 1611 0.115 - 0.172: 671 0.172 - 0.230: 148 0.230 - 0.287: 9 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1' U 1 21 " pdb=" O4' U 1 21 " pdb=" C2' U 1 21 " pdb=" N1 U 1 21 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA GLU I 85 " pdb=" N GLU I 85 " pdb=" C GLU I 85 " pdb=" CB GLU I 85 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA TYR I 140 " pdb=" N TYR I 140 " pdb=" C TYR I 140 " pdb=" CB TYR I 140 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4500 not shown) Planarity restraints: 5002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 127 " -0.064 2.00e-02 2.50e+03 1.20e-01 1.44e+02 pdb=" CD GLU D 127 " 0.208 2.00e-02 2.50e+03 pdb=" OE1 GLU D 127 " -0.069 2.00e-02 2.50e+03 pdb=" OE2 GLU D 127 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 403 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C SER G 403 " -0.043 2.00e-02 2.50e+03 pdb=" O SER G 403 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO G 404 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 7 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C LYS I 7 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS I 7 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO I 8 " 0.013 2.00e-02 2.50e+03 ... (remaining 4999 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 30 1.99 - 2.71: 1050 2.71 - 3.44: 37507 3.44 - 4.17: 66348 4.17 - 4.90: 117979 Nonbonded interactions: 222914 Sorted by model distance: nonbonded pdb=" CG TYR H 5 " pdb=" CD1 ILE H 199 " model vdw 1.256 3.680 nonbonded pdb=" CE MET F 346 " pdb=" N1 U 1 35 " model vdw 1.271 3.540 nonbonded pdb=" CD1 ILE G 42 " pdb=" CB LEU G 56 " model vdw 1.282 3.860 nonbonded pdb=" O ASP G 48 " pdb=" ND2 ASN G 131 " model vdw 1.347 3.120 nonbonded pdb=" CE MET F 220 " pdb=" N7 G 1 41 " model vdw 1.376 3.540 ... (remaining 222909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 232 or resid 236 through 351 or resid 361 throug \ h 393)) selection = (chain 'J' and (resid 1 through 162 or resid 195 through 351 or resid 361 throug \ h 393)) } 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.930 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.014 0.406 29816 Z= 1.064 Angle : 1.740 9.218 40742 Z= 1.230 Chirality : 0.085 0.287 4503 Planarity : 0.004 0.120 5002 Dihedral : 17.072 178.905 11252 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 3.91 % Allowed : 14.76 % Favored : 81.32 % Rotamer: Outliers : 2.17 % Allowed : 6.20 % Favored : 91.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 6.06 % Twisted General : 2.55 % 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: -4.83 (0.11), residues: 3400 helix: -2.66 (0.14), residues: 880 sheet: -1.93 (0.21), residues: 477 loop : -4.02 (0.11), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 178 TYR 0.025 0.002 TYR I 101 PHE 0.019 0.002 PHE I 144 TRP 0.031 0.002 TRP A 24 HIS 0.009 0.002 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.01367 (29814) covalent geometry : angle 1.74020 (40742) hydrogen bonds : bond 0.21182 ( 753) hydrogen bonds : angle 8.79432 ( 2089) Misc. bond : bond 0.28916 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 643 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 42 GLN cc_start: 0.7782 (pt0) cc_final: 0.7581 (pt0) REVERT: A 293 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5839 (p0) REVERT: B 43 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: B 134 MET cc_start: 0.8398 (mtm) cc_final: 0.8003 (mtp) REVERT: B 333 ASP cc_start: 0.8388 (m-30) cc_final: 0.8150 (m-30) REVERT: C 210 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7435 (ptp90) REVERT: C 244 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8194 (ttm170) REVERT: C 324 LYS cc_start: 0.7295 (tppt) cc_final: 0.6639 (tptm) REVERT: D 71 HIS cc_start: 0.6693 (m-70) cc_final: 0.6329 (t-170) REVERT: D 120 GLU cc_start: 0.8012 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 291 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7127 (ttp-170) REVERT: F 6 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7074 (m-40) REVERT: F 71 HIS cc_start: 0.6126 (t-90) cc_final: 0.5684 (t-90) REVERT: F 88 SER cc_start: 0.7864 (t) cc_final: 0.7389 (p) REVERT: F 195 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7686 (ttmm) REVERT: F 210 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7324 (ttm-80) REVERT: F 263 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8105 (tptt) REVERT: F 308 SER cc_start: 0.8416 (m) cc_final: 0.7847 (t) REVERT: G 47 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6871 (t) REVERT: G 190 ASN cc_start: 0.7309 (t0) cc_final: 0.6925 (m110) REVERT: G 205 ASP cc_start: 0.7884 (p0) cc_final: 0.7615 (p0) REVERT: G 469 THR cc_start: 0.7726 (p) cc_final: 0.7351 (p) REVERT: G 613 PHE cc_start: 0.7354 (m-80) cc_final: 0.6850 (m-80) REVERT: H 77 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7318 (mt0) REVERT: H 81 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8369 (pp) REVERT: H 127 LEU cc_start: 0.6116 (mm) cc_final: 0.5639 (pp) REVERT: I 1 MET cc_start: 0.0525 (tpt) cc_final: 0.0163 (mmm) REVERT: I 57 THR cc_start: 0.5045 (m) cc_final: 0.4769 (p) REVERT: I 130 LEU cc_start: 0.2321 (OUTLIER) cc_final: 0.1985 (mm) REVERT: I 198 CYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5413 (t) REVERT: I 272 GLU cc_start: 0.7840 (pt0) cc_final: 0.7570 (mp0) REVERT: I 383 ASP cc_start: 0.7937 (p0) cc_final: 0.7729 (p0) REVERT: I 386 ASN cc_start: 0.8150 (t0) cc_final: 0.7949 (t0) REVERT: J 43 ASP cc_start: 0.7734 (m-30) cc_final: 0.7326 (m-30) REVERT: J 47 ASN cc_start: 0.7750 (p0) cc_final: 0.7530 (m-40) REVERT: J 217 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7294 (tttt) outliers start: 66 outliers final: 25 residues processed: 694 average time/residue: 0.2094 time to fit residues: 220.7177 Evaluate side-chains 357 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 276 PRO Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 276 PRO Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 533 PRO Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 218 ASN B 183 ASN B 311 GLN B 312 GLN C 104 ASN C 174 ASN C 311 GLN C 323 ASN D 174 ASN D 183 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS E 241 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN F 183 ASN F 218 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS G 180 GLN G 196 ASN G 227 GLN G 384 ASN G 392 ASN G 444 GLN H 88 ASN H 132 GLN I 80 GLN I 84 ASN I 151 HIS I 265 HIS I 386 ASN J 46 HIS J 95 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.153074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118199 restraints weight = 44368.587| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.93 r_work: 0.3098 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29816 Z= 0.168 Angle : 0.842 12.070 40742 Z= 0.440 Chirality : 0.048 0.289 4503 Planarity : 0.005 0.094 5002 Dihedral : 15.904 175.366 4722 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.97 % Allowed : 13.21 % Favored : 85.82 % Rotamer: Outliers : 3.12 % Allowed : 11.58 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 5.45 % Twisted General : 1.69 % 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: -3.88 (0.13), residues: 3400 helix: -1.44 (0.17), residues: 904 sheet: -1.00 (0.23), residues: 474 loop : -3.75 (0.11), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 5 TYR 0.025 0.002 TYR J 169 PHE 0.022 0.002 PHE G 433 TRP 0.039 0.002 TRP A 24 HIS 0.011 0.001 HIS G 490 Details of bonding type rmsd covalent geometry : bond 0.00367 (29814) covalent geometry : angle 0.84219 (40742) hydrogen bonds : bond 0.04169 ( 753) hydrogen bonds : angle 5.64222 ( 2089) Misc. bond : bond 0.00310 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 371 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.6631 (OUTLIER) cc_final: 0.6412 (m) REVERT: A 114 GLN cc_start: 0.8027 (tp40) cc_final: 0.7686 (tp-100) REVERT: A 293 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6590 (p0) REVERT: B 17 ASP cc_start: 0.8486 (p0) cc_final: 0.8166 (p0) REVERT: B 185 LYS cc_start: 0.5446 (pttm) cc_final: 0.5125 (mtmt) REVERT: C 252 ASP cc_start: 0.8216 (m-30) cc_final: 0.7923 (t0) REVERT: C 324 LYS cc_start: 0.7121 (tppt) cc_final: 0.6707 (mmtt) REVERT: D 71 HIS cc_start: 0.7585 (m-70) cc_final: 0.7239 (t-170) REVERT: F 188 SER cc_start: 0.8686 (m) cc_final: 0.8469 (p) REVERT: F 210 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7984 (ttm170) REVERT: F 263 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8525 (tttp) REVERT: G 5 LYS cc_start: 0.6397 (mptt) cc_final: 0.5947 (mmtt) REVERT: G 19 LEU cc_start: 0.8412 (tp) cc_final: 0.7892 (tp) REVERT: G 23 PHE cc_start: 0.8148 (m-80) cc_final: 0.7781 (m-80) REVERT: G 190 ASN cc_start: 0.7593 (t0) cc_final: 0.7103 (m110) REVERT: G 231 ASP cc_start: 0.7612 (m-30) cc_final: 0.6871 (p0) REVERT: H 16 ASN cc_start: 0.8426 (t0) cc_final: 0.8164 (t0) REVERT: H 102 ARG cc_start: 0.6853 (ptp-170) cc_final: 0.6368 (ttt-90) REVERT: H 127 LEU cc_start: 0.5887 (mm) cc_final: 0.5535 (pp) REVERT: H 160 ASN cc_start: 0.7441 (m-40) cc_final: 0.7153 (m110) REVERT: H 197 PRO cc_start: 0.8744 (Cg_endo) cc_final: 0.8197 (Cg_exo) REVERT: I 3 LEU cc_start: 0.4865 (tp) cc_final: 0.3760 (mt) REVERT: I 66 ASN cc_start: 0.6228 (m-40) cc_final: 0.5152 (t0) REVERT: I 84 ASN cc_start: 0.4953 (OUTLIER) cc_final: 0.4537 (t0) REVERT: I 198 CYS cc_start: 0.6382 (OUTLIER) cc_final: 0.5834 (t) REVERT: I 217 LYS cc_start: 0.7305 (mtpt) cc_final: 0.7009 (mttp) REVERT: I 272 GLU cc_start: 0.8103 (pt0) cc_final: 0.7712 (mp0) REVERT: I 386 ASN cc_start: 0.8331 (t0) cc_final: 0.8089 (t0) REVERT: J 43 ASP cc_start: 0.7932 (m-30) cc_final: 0.7509 (m-30) REVERT: J 47 ASN cc_start: 0.8220 (p0) cc_final: 0.7838 (m-40) REVERT: J 85 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7922 (mp0) REVERT: J 108 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7398 (m) REVERT: J 153 HIS cc_start: 0.5837 (OUTLIER) cc_final: 0.5532 (p90) REVERT: J 323 MET cc_start: 0.4884 (tpp) cc_final: 0.4642 (tpp) REVERT: J 367 PHE cc_start: 0.7069 (m-10) cc_final: 0.6868 (m-10) outliers start: 95 outliers final: 45 residues processed: 443 average time/residue: 0.1808 time to fit residues: 128.4304 Evaluate side-chains 331 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 279 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 181 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 308 optimal weight: 4.9990 chunk 121 optimal weight: 0.0030 chunk 235 optimal weight: 9.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 110 GLN A 311 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS G 131 ASN ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 548 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 73 HIS I 31 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112597 restraints weight = 44624.768| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.12 r_work: 0.3026 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29816 Z= 0.219 Angle : 0.819 11.896 40742 Z= 0.428 Chirality : 0.049 0.273 4503 Planarity : 0.005 0.061 5002 Dihedral : 15.481 177.643 4679 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.82 % Allowed : 15.65 % Favored : 83.53 % Rotamer: Outliers : 3.41 % Allowed : 13.98 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 4.85 % Twisted General : 1.56 % 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: -3.66 (0.13), residues: 3400 helix: -1.15 (0.17), residues: 905 sheet: -0.98 (0.22), residues: 491 loop : -3.66 (0.11), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 283 TYR 0.020 0.002 TYR G 543 PHE 0.023 0.002 PHE I 238 TRP 0.026 0.002 TRP I 203 HIS 0.018 0.002 HIS H 73 Details of bonding type rmsd covalent geometry : bond 0.00508 (29814) covalent geometry : angle 0.81857 (40742) hydrogen bonds : bond 0.04278 ( 753) hydrogen bonds : angle 5.34965 ( 2089) Misc. bond : bond 0.00321 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 309 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8099 (tp40) cc_final: 0.7776 (tp-100) REVERT: A 293 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7186 (p0) REVERT: A 307 PHE cc_start: 0.8294 (m-10) cc_final: 0.7882 (m-10) REVERT: B 17 ASP cc_start: 0.8624 (p0) cc_final: 0.8379 (p0) REVERT: C 252 ASP cc_start: 0.8203 (m-30) cc_final: 0.7855 (t0) REVERT: D 71 HIS cc_start: 0.7646 (m-70) cc_final: 0.7381 (m-70) REVERT: E 252 ASP cc_start: 0.8649 (t0) cc_final: 0.8270 (t0) REVERT: F 188 SER cc_start: 0.8860 (m) cc_final: 0.8609 (p) REVERT: F 263 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8736 (tttp) REVERT: G 5 LYS cc_start: 0.6454 (mptt) cc_final: 0.6021 (tmtt) REVERT: G 23 PHE cc_start: 0.8101 (m-80) cc_final: 0.7723 (m-80) REVERT: G 231 ASP cc_start: 0.7737 (m-30) cc_final: 0.7262 (p0) REVERT: H 16 ASN cc_start: 0.8583 (t0) cc_final: 0.8079 (t0) REVERT: H 81 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8558 (pp) REVERT: H 88 ASN cc_start: 0.7291 (m-40) cc_final: 0.6689 (t0) REVERT: H 93 PRO cc_start: 0.5768 (Cg_exo) cc_final: 0.5553 (Cg_endo) REVERT: H 127 LEU cc_start: 0.5991 (mm) cc_final: 0.5665 (pp) REVERT: H 164 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6680 (mtp180) REVERT: H 181 PHE cc_start: 0.4688 (OUTLIER) cc_final: 0.3782 (p90) REVERT: H 194 GLN cc_start: 0.7434 (pp30) cc_final: 0.7144 (pp30) REVERT: I 3 LEU cc_start: 0.5091 (tp) cc_final: 0.3727 (mt) REVERT: I 198 CYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6370 (t) REVERT: I 217 LYS cc_start: 0.7453 (mtpt) cc_final: 0.7138 (mttp) REVERT: I 272 GLU cc_start: 0.8204 (pt0) cc_final: 0.7743 (mp0) REVERT: J 43 ASP cc_start: 0.7915 (m-30) cc_final: 0.7567 (m-30) REVERT: J 47 ASN cc_start: 0.8355 (p0) cc_final: 0.7955 (m110) REVERT: J 108 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7889 (m) REVERT: J 153 HIS cc_start: 0.6006 (OUTLIER) cc_final: 0.5718 (p90) REVERT: J 308 GLU cc_start: 0.6012 (tm-30) cc_final: 0.5711 (tm-30) REVERT: J 323 MET cc_start: 0.5242 (tpp) cc_final: 0.5018 (tpp) outliers start: 104 outliers final: 58 residues processed: 396 average time/residue: 0.1691 time to fit residues: 109.3338 Evaluate side-chains 325 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 274 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 55 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 132 GLN I 84 ASN I 154 ASN I 252 HIS I 296 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112581 restraints weight = 44322.524| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.80 r_work: 0.3028 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29816 Z= 0.199 Angle : 0.785 11.451 40742 Z= 0.410 Chirality : 0.047 0.251 4503 Planarity : 0.005 0.060 5002 Dihedral : 15.215 176.967 4677 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 14.62 % Favored : 84.53 % Rotamer: Outliers : 3.87 % Allowed : 14.27 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 4.24 % Twisted General : 1.32 % 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: -3.50 (0.13), residues: 3400 helix: -1.06 (0.17), residues: 926 sheet: -0.95 (0.22), residues: 511 loop : -3.55 (0.12), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 286 TYR 0.022 0.002 TYR G 197 PHE 0.017 0.002 PHE A 89 TRP 0.028 0.001 TRP I 203 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00459 (29814) covalent geometry : angle 0.78452 (40742) hydrogen bonds : bond 0.03864 ( 753) hydrogen bonds : angle 5.21480 ( 2089) Misc. bond : bond 0.00216 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 288 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8237 (tp40) cc_final: 0.7949 (tp-100) REVERT: A 212 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8662 (m) REVERT: A 307 PHE cc_start: 0.8315 (m-10) cc_final: 0.7875 (m-10) REVERT: B 17 ASP cc_start: 0.8659 (p0) cc_final: 0.8380 (p0) REVERT: B 138 ASN cc_start: 0.8596 (p0) cc_final: 0.8076 (p0) REVERT: C 252 ASP cc_start: 0.8142 (m-30) cc_final: 0.7833 (t0) REVERT: D 71 HIS cc_start: 0.7762 (m-70) cc_final: 0.7528 (m-70) REVERT: E 252 ASP cc_start: 0.8625 (t0) cc_final: 0.8258 (t0) REVERT: E 333 ASP cc_start: 0.8212 (m-30) cc_final: 0.7958 (m-30) REVERT: F 37 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7224 (mtp180) REVERT: F 135 ASN cc_start: 0.8483 (p0) cc_final: 0.8192 (p0) REVERT: F 188 SER cc_start: 0.8794 (m) cc_final: 0.8547 (p) REVERT: G 5 LYS cc_start: 0.6604 (mptt) cc_final: 0.6185 (tmtt) REVERT: G 23 PHE cc_start: 0.8050 (m-80) cc_final: 0.7736 (m-80) REVERT: G 231 ASP cc_start: 0.7308 (m-30) cc_final: 0.7085 (p0) REVERT: G 622 TYR cc_start: 0.7914 (p90) cc_final: 0.7637 (p90) REVERT: H 16 ASN cc_start: 0.8658 (t0) cc_final: 0.8210 (t0) REVERT: H 78 MET cc_start: 0.7646 (tpp) cc_final: 0.7430 (tpp) REVERT: H 81 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8593 (pp) REVERT: H 88 ASN cc_start: 0.7296 (m-40) cc_final: 0.6687 (t0) REVERT: H 105 GLN cc_start: 0.8755 (tt0) cc_final: 0.8439 (tt0) REVERT: H 181 PHE cc_start: 0.4378 (OUTLIER) cc_final: 0.3945 (p90) REVERT: H 190 GLU cc_start: 0.5654 (pt0) cc_final: 0.5310 (pt0) REVERT: I 84 ASN cc_start: 0.4761 (OUTLIER) cc_final: 0.4555 (t0) REVERT: I 110 ARG cc_start: 0.5799 (tpm170) cc_final: 0.4318 (tpm170) REVERT: I 198 CYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6880 (t) REVERT: I 217 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7207 (mttp) REVERT: I 239 SER cc_start: 0.4704 (m) cc_final: 0.4452 (t) REVERT: I 272 GLU cc_start: 0.8210 (pt0) cc_final: 0.7777 (mp0) REVERT: I 326 LEU cc_start: 0.8405 (mt) cc_final: 0.8201 (mp) REVERT: J 43 ASP cc_start: 0.7931 (m-30) cc_final: 0.7647 (m-30) REVERT: J 100 LYS cc_start: 0.8567 (mttm) cc_final: 0.8288 (mmmt) REVERT: J 308 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5801 (tm-30) REVERT: J 323 MET cc_start: 0.5269 (tpp) cc_final: 0.5041 (tpp) outliers start: 118 outliers final: 73 residues processed: 385 average time/residue: 0.1801 time to fit residues: 112.9355 Evaluate side-chains 343 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 264 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 39 ASN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 58 optimal weight: 0.0670 chunk 232 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 254 optimal weight: 8.9990 chunk 270 optimal weight: 30.0000 chunk 22 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 2.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN G 226 HIS ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112986 restraints weight = 44179.618| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.76 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29816 Z= 0.168 Angle : 0.759 11.184 40742 Z= 0.394 Chirality : 0.046 0.311 4503 Planarity : 0.005 0.063 5002 Dihedral : 14.988 177.960 4668 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.79 % Allowed : 14.97 % Favored : 84.24 % Rotamer: Outliers : 3.58 % Allowed : 15.55 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.64 % Twisted General : 1.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.13), residues: 3400 helix: -0.95 (0.17), residues: 930 sheet: -0.82 (0.22), residues: 511 loop : -3.48 (0.12), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 286 TYR 0.021 0.001 TYR G 197 PHE 0.015 0.001 PHE I 240 TRP 0.028 0.001 TRP I 203 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00381 (29814) covalent geometry : angle 0.75937 (40742) hydrogen bonds : bond 0.03619 ( 753) hydrogen bonds : angle 5.12237 ( 2089) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 296 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8148 (tp40) cc_final: 0.7856 (tp-100) REVERT: A 307 PHE cc_start: 0.8247 (m-10) cc_final: 0.7849 (m-10) REVERT: B 17 ASP cc_start: 0.8624 (p0) cc_final: 0.8324 (p0) REVERT: B 138 ASN cc_start: 0.8552 (p0) cc_final: 0.8280 (p0) REVERT: C 252 ASP cc_start: 0.8153 (m-30) cc_final: 0.7833 (t0) REVERT: C 291 ARG cc_start: 0.7400 (ttt-90) cc_final: 0.7181 (ttp80) REVERT: C 347 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: D 71 HIS cc_start: 0.7757 (m-70) cc_final: 0.7552 (m170) REVERT: E 252 ASP cc_start: 0.8583 (t0) cc_final: 0.8210 (t0) REVERT: E 333 ASP cc_start: 0.8155 (m-30) cc_final: 0.7915 (m-30) REVERT: F 135 ASN cc_start: 0.8407 (p0) cc_final: 0.8143 (p0) REVERT: F 188 SER cc_start: 0.8755 (m) cc_final: 0.8521 (p) REVERT: G 19 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7744 (tt) REVERT: G 23 PHE cc_start: 0.8107 (m-80) cc_final: 0.7769 (m-80) REVERT: G 231 ASP cc_start: 0.7238 (m-30) cc_final: 0.7038 (p0) REVERT: G 622 TYR cc_start: 0.7945 (p90) cc_final: 0.7668 (p90) REVERT: H 16 ASN cc_start: 0.8635 (t0) cc_final: 0.8206 (t0) REVERT: H 33 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: H 81 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8579 (pp) REVERT: H 88 ASN cc_start: 0.7329 (m-40) cc_final: 0.6716 (t0) REVERT: H 105 GLN cc_start: 0.8748 (tt0) cc_final: 0.8384 (tt0) REVERT: H 176 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5456 (pt0) REVERT: I 3 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3901 (mt) REVERT: I 105 THR cc_start: 0.7565 (p) cc_final: 0.6755 (p) REVERT: I 110 ARG cc_start: 0.5612 (tpm170) cc_final: 0.5113 (mmm160) REVERT: I 217 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7244 (mttp) REVERT: I 272 GLU cc_start: 0.8196 (pt0) cc_final: 0.7790 (mp0) REVERT: I 326 LEU cc_start: 0.8413 (mt) cc_final: 0.8212 (mp) REVERT: J 43 ASP cc_start: 0.7958 (m-30) cc_final: 0.7655 (m-30) REVERT: J 100 LYS cc_start: 0.8530 (mttm) cc_final: 0.8293 (mmmt) REVERT: J 308 GLU cc_start: 0.6090 (tm-30) cc_final: 0.5772 (tm-30) REVERT: J 348 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4775 (pp) outliers start: 109 outliers final: 64 residues processed: 382 average time/residue: 0.1735 time to fit residues: 108.3363 Evaluate side-chains 337 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 72 GLN H 148 HIS I 145 GLN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111209 restraints weight = 44119.458| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.87 r_work: 0.3023 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29816 Z= 0.213 Angle : 0.797 15.163 40742 Z= 0.412 Chirality : 0.047 0.235 4503 Planarity : 0.006 0.069 5002 Dihedral : 14.923 178.544 4665 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.68 % Favored : 83.56 % Rotamer: Outliers : 3.87 % Allowed : 16.60 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.13), residues: 3400 helix: -0.98 (0.17), residues: 947 sheet: -0.63 (0.23), residues: 492 loop : -3.43 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 286 TYR 0.018 0.002 TYR J 169 PHE 0.019 0.002 PHE F 89 TRP 0.024 0.002 TRP I 203 HIS 0.007 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00494 (29814) covalent geometry : angle 0.79676 (40742) hydrogen bonds : bond 0.03891 ( 753) hydrogen bonds : angle 5.14224 ( 2089) Misc. bond : bond 0.00191 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 278 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8139 (tp40) cc_final: 0.7844 (tp-100) REVERT: A 212 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8720 (m) REVERT: A 307 PHE cc_start: 0.8285 (m-10) cc_final: 0.7874 (m-10) REVERT: B 138 ASN cc_start: 0.8588 (p0) cc_final: 0.8012 (p0) REVERT: C 252 ASP cc_start: 0.8168 (m-30) cc_final: 0.7848 (t0) REVERT: C 291 ARG cc_start: 0.7465 (ttt-90) cc_final: 0.7209 (ttp80) REVERT: C 347 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: D 71 HIS cc_start: 0.7766 (m-70) cc_final: 0.7432 (t-170) REVERT: E 252 ASP cc_start: 0.8605 (t0) cc_final: 0.8254 (t0) REVERT: E 333 ASP cc_start: 0.8216 (m-30) cc_final: 0.7964 (m-30) REVERT: F 188 SER cc_start: 0.8828 (m) cc_final: 0.8602 (p) REVERT: G 19 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7986 (tt) REVERT: G 21 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6867 (ptm160) REVERT: G 622 TYR cc_start: 0.7851 (p90) cc_final: 0.7552 (p90) REVERT: H 16 ASN cc_start: 0.8647 (t0) cc_final: 0.8367 (t0) REVERT: H 88 ASN cc_start: 0.7407 (m-40) cc_final: 0.6776 (t0) REVERT: H 176 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.3881 (mm-30) REVERT: I 3 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.4177 (mt) REVERT: I 217 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7294 (mttp) REVERT: I 272 GLU cc_start: 0.8240 (pt0) cc_final: 0.7818 (mp0) REVERT: I 311 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8647 (tt) REVERT: J 43 ASP cc_start: 0.7993 (m-30) cc_final: 0.7739 (m-30) REVERT: J 100 LYS cc_start: 0.8541 (mttm) cc_final: 0.8235 (mmmt) REVERT: J 105 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6295 (m) REVERT: J 308 GLU cc_start: 0.6119 (tm-30) cc_final: 0.5846 (tm-30) REVERT: J 323 MET cc_start: 0.4413 (tpp) cc_final: 0.4113 (tpp) outliers start: 118 outliers final: 77 residues processed: 373 average time/residue: 0.1683 time to fit residues: 103.4684 Evaluate side-chains 341 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 256 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 39 ASN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 289 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 84 optimal weight: 0.0020 chunk 143 optimal weight: 0.3980 chunk 179 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 overall best weight: 1.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 143 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113790 restraints weight = 44238.271| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.76 r_work: 0.3050 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29816 Z= 0.155 Angle : 0.752 13.044 40742 Z= 0.388 Chirality : 0.045 0.228 4503 Planarity : 0.005 0.072 5002 Dihedral : 14.767 177.847 4663 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.85 % Favored : 84.50 % Rotamer: Outliers : 3.38 % Allowed : 17.68 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.10 % 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: -3.13 (0.14), residues: 3400 helix: -0.78 (0.17), residues: 932 sheet: -0.79 (0.22), residues: 516 loop : -3.29 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 286 TYR 0.018 0.001 TYR I 390 PHE 0.015 0.001 PHE A 89 TRP 0.026 0.001 TRP A 24 HIS 0.007 0.001 HIS H 148 Details of bonding type rmsd covalent geometry : bond 0.00348 (29814) covalent geometry : angle 0.75171 (40742) hydrogen bonds : bond 0.03382 ( 753) hydrogen bonds : angle 5.03387 ( 2089) Misc. bond : bond 0.00189 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 280 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8108 (tp40) cc_final: 0.7826 (tp-100) REVERT: A 212 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 307 PHE cc_start: 0.8253 (m-10) cc_final: 0.7865 (m-10) REVERT: B 6 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8260 (t0) REVERT: B 138 ASN cc_start: 0.8437 (p0) cc_final: 0.7871 (p0) REVERT: C 252 ASP cc_start: 0.8168 (m-30) cc_final: 0.7849 (t0) REVERT: C 347 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: D 71 HIS cc_start: 0.7717 (m-70) cc_final: 0.7421 (t-170) REVERT: E 252 ASP cc_start: 0.8568 (t0) cc_final: 0.8203 (t0) REVERT: F 188 SER cc_start: 0.8740 (m) cc_final: 0.8530 (p) REVERT: G 19 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7915 (tt) REVERT: G 21 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6831 (ptm160) REVERT: G 622 TYR cc_start: 0.7840 (p90) cc_final: 0.7516 (p90) REVERT: H 16 ASN cc_start: 0.8644 (t0) cc_final: 0.8367 (t0) REVERT: H 88 ASN cc_start: 0.7432 (m-40) cc_final: 0.6810 (t0) REVERT: I 3 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4040 (mt) REVERT: I 217 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7213 (mttm) REVERT: I 272 GLU cc_start: 0.8166 (pt0) cc_final: 0.7817 (mp0) REVERT: J 43 ASP cc_start: 0.7902 (m-30) cc_final: 0.7619 (m-30) REVERT: J 100 LYS cc_start: 0.8484 (mttm) cc_final: 0.8203 (mmmt) REVERT: J 105 THR cc_start: 0.6536 (OUTLIER) cc_final: 0.6226 (m) REVERT: J 308 GLU cc_start: 0.6070 (tm-30) cc_final: 0.5789 (tm-30) REVERT: J 323 MET cc_start: 0.4425 (tpp) cc_final: 0.4136 (tpp) outliers start: 103 outliers final: 69 residues processed: 365 average time/residue: 0.1714 time to fit residues: 103.2240 Evaluate side-chains 341 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 39 ASN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 226 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 82 optimal weight: 0.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN ** J 207 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.151090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115795 restraints weight = 44415.317| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.76 r_work: 0.3095 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29816 Z= 0.136 Angle : 0.731 13.474 40742 Z= 0.375 Chirality : 0.045 0.320 4503 Planarity : 0.005 0.075 5002 Dihedral : 14.596 177.583 4661 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.71 % Favored : 84.68 % Rotamer: Outliers : 3.18 % Allowed : 18.18 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 1.01 % 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: -2.97 (0.14), residues: 3400 helix: -0.65 (0.17), residues: 933 sheet: -0.71 (0.23), residues: 521 loop : -3.19 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 110 TYR 0.018 0.001 TYR I 390 PHE 0.014 0.001 PHE I 240 TRP 0.027 0.001 TRP A 24 HIS 0.008 0.001 HIS H 148 Details of bonding type rmsd covalent geometry : bond 0.00297 (29814) covalent geometry : angle 0.73109 (40742) hydrogen bonds : bond 0.03161 ( 753) hydrogen bonds : angle 4.94662 ( 2089) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 287 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 PHE cc_start: 0.8122 (m-10) cc_final: 0.7757 (m-10) REVERT: A 346 MET cc_start: 0.7169 (tpp) cc_final: 0.5494 (tpp) REVERT: B 6 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8176 (t0) REVERT: B 138 ASN cc_start: 0.8297 (p0) cc_final: 0.7870 (t0) REVERT: C 252 ASP cc_start: 0.8157 (m-30) cc_final: 0.7842 (t0) REVERT: C 347 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: D 71 HIS cc_start: 0.7721 (m-70) cc_final: 0.7439 (t-170) REVERT: D 316 TYR cc_start: 0.8970 (m-80) cc_final: 0.8758 (m-80) REVERT: E 252 ASP cc_start: 0.8543 (t0) cc_final: 0.8220 (t0) REVERT: F 188 SER cc_start: 0.8816 (m) cc_final: 0.8571 (p) REVERT: G 5 LYS cc_start: 0.6797 (mptt) cc_final: 0.6575 (tttm) REVERT: G 19 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (tt) REVERT: G 21 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6674 (ptm160) REVERT: G 448 GLU cc_start: 0.7528 (pt0) cc_final: 0.7230 (pp20) REVERT: G 622 TYR cc_start: 0.7781 (p90) cc_final: 0.7476 (p90) REVERT: H 16 ASN cc_start: 0.8618 (t0) cc_final: 0.8354 (t0) REVERT: H 88 ASN cc_start: 0.7404 (m-40) cc_final: 0.6774 (t0) REVERT: H 194 GLN cc_start: 0.7538 (pp30) cc_final: 0.6951 (tm-30) REVERT: I 3 LEU cc_start: 0.4400 (OUTLIER) cc_final: 0.3906 (mt) REVERT: I 217 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7125 (mttm) REVERT: I 272 GLU cc_start: 0.8064 (pt0) cc_final: 0.7772 (mp0) REVERT: J 43 ASP cc_start: 0.7927 (m-30) cc_final: 0.7605 (m-30) REVERT: J 100 LYS cc_start: 0.8435 (mttm) cc_final: 0.8189 (mmmt) REVERT: J 105 THR cc_start: 0.6413 (OUTLIER) cc_final: 0.6108 (m) REVERT: J 308 GLU cc_start: 0.6051 (tm-30) cc_final: 0.5710 (tm-30) REVERT: J 323 MET cc_start: 0.4615 (tpp) cc_final: 0.4316 (tpp) REVERT: J 387 ARG cc_start: 0.5554 (ptm-80) cc_final: 0.5035 (ptm-80) outliers start: 97 outliers final: 70 residues processed: 366 average time/residue: 0.1675 time to fit residues: 101.0825 Evaluate side-chains 341 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 334 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 321 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 325 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 270 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS H 160 ASN I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113337 restraints weight = 44336.419| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.89 r_work: 0.3031 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29816 Z= 0.195 Angle : 0.778 13.520 40742 Z= 0.400 Chirality : 0.046 0.286 4503 Planarity : 0.005 0.075 5002 Dihedral : 14.613 177.998 4661 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 15.53 % Favored : 83.88 % Rotamer: Outliers : 3.08 % Allowed : 18.93 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 0.95 % 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: -2.98 (0.14), residues: 3400 helix: -0.70 (0.17), residues: 934 sheet: -0.67 (0.22), residues: 524 loop : -3.20 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 286 TYR 0.020 0.002 TYR E 275 PHE 0.018 0.002 PHE F 89 TRP 0.022 0.001 TRP J 142 HIS 0.027 0.001 HIS J 153 Details of bonding type rmsd covalent geometry : bond 0.00452 (29814) covalent geometry : angle 0.77827 (40742) hydrogen bonds : bond 0.03648 ( 753) hydrogen bonds : angle 4.99570 ( 2089) Misc. bond : bond 0.00236 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 273 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8701 (m) REVERT: A 307 PHE cc_start: 0.8253 (m-10) cc_final: 0.7847 (m-10) REVERT: A 346 MET cc_start: 0.7459 (tpp) cc_final: 0.5835 (tpp) REVERT: B 6 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (t0) REVERT: B 138 ASN cc_start: 0.8451 (p0) cc_final: 0.7921 (p0) REVERT: C 252 ASP cc_start: 0.8189 (m-30) cc_final: 0.7875 (t0) REVERT: C 347 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8529 (m-80) REVERT: D 71 HIS cc_start: 0.7788 (m-70) cc_final: 0.7498 (t-170) REVERT: E 252 ASP cc_start: 0.8565 (t0) cc_final: 0.8207 (t0) REVERT: F 43 MET cc_start: 0.6330 (mpp) cc_final: 0.5830 (mpp) REVERT: F 188 SER cc_start: 0.8840 (m) cc_final: 0.8617 (p) REVERT: G 21 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6687 (ptm160) REVERT: G 622 TYR cc_start: 0.7905 (p90) cc_final: 0.7513 (p90) REVERT: H 16 ASN cc_start: 0.8648 (t0) cc_final: 0.8300 (t0) REVERT: H 88 ASN cc_start: 0.7431 (m-40) cc_final: 0.6777 (t0) REVERT: H 107 ILE cc_start: 0.8563 (mm) cc_final: 0.8323 (mt) REVERT: H 194 GLN cc_start: 0.7545 (pp30) cc_final: 0.6815 (tm-30) REVERT: I 3 LEU cc_start: 0.4735 (OUTLIER) cc_final: 0.4189 (mt) REVERT: I 217 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7217 (mttm) REVERT: I 272 GLU cc_start: 0.8132 (pt0) cc_final: 0.7821 (mp0) REVERT: J 43 ASP cc_start: 0.8000 (m-30) cc_final: 0.7796 (m-30) REVERT: J 105 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6381 (m) REVERT: J 308 GLU cc_start: 0.6052 (tm-30) cc_final: 0.5734 (tm-30) REVERT: J 387 ARG cc_start: 0.5610 (ptm-80) cc_final: 0.5320 (ptm-80) outliers start: 94 outliers final: 77 residues processed: 352 average time/residue: 0.1737 time to fit residues: 100.6329 Evaluate side-chains 346 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 263 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS H 160 ASN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS J 225 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113766 restraints weight = 44338.654| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.76 r_work: 0.3048 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29816 Z= 0.173 Angle : 0.769 14.465 40742 Z= 0.395 Chirality : 0.046 0.271 4503 Planarity : 0.005 0.074 5002 Dihedral : 14.598 177.905 4661 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.18 % Favored : 84.32 % Rotamer: Outliers : 3.12 % Allowed : 19.06 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 0.98 % 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: -2.97 (0.14), residues: 3400 helix: -0.73 (0.17), residues: 939 sheet: -0.68 (0.22), residues: 527 loop : -3.17 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 110 TYR 0.018 0.002 TYR A 175 PHE 0.021 0.001 PHE I 40 TRP 0.023 0.001 TRP J 142 HIS 0.024 0.001 HIS F 315 Details of bonding type rmsd covalent geometry : bond 0.00397 (29814) covalent geometry : angle 0.76945 (40742) hydrogen bonds : bond 0.03479 ( 753) hydrogen bonds : angle 4.99408 ( 2089) Misc. bond : bond 0.00159 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 271 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8700 (m) REVERT: A 307 PHE cc_start: 0.8243 (m-10) cc_final: 0.7845 (m-10) REVERT: A 346 MET cc_start: 0.7376 (tpp) cc_final: 0.5748 (tpp) REVERT: B 6 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8186 (t0) REVERT: B 138 ASN cc_start: 0.8423 (p0) cc_final: 0.7774 (t0) REVERT: C 252 ASP cc_start: 0.8173 (m-30) cc_final: 0.7866 (t0) REVERT: C 347 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: D 71 HIS cc_start: 0.7775 (m-70) cc_final: 0.7496 (t-170) REVERT: E 252 ASP cc_start: 0.8557 (t0) cc_final: 0.8204 (t0) REVERT: F 43 MET cc_start: 0.6177 (mpp) cc_final: 0.5701 (mpp) REVERT: F 188 SER cc_start: 0.8843 (m) cc_final: 0.8625 (p) REVERT: G 21 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6726 (ptm160) REVERT: G 622 TYR cc_start: 0.7859 (p90) cc_final: 0.7532 (p90) REVERT: H 16 ASN cc_start: 0.8662 (t0) cc_final: 0.8296 (t0) REVERT: H 88 ASN cc_start: 0.7413 (m-40) cc_final: 0.6781 (t0) REVERT: H 107 ILE cc_start: 0.8524 (mm) cc_final: 0.8293 (mt) REVERT: H 194 GLN cc_start: 0.7503 (pp30) cc_final: 0.6754 (tm-30) REVERT: I 3 LEU cc_start: 0.4853 (OUTLIER) cc_final: 0.4254 (mt) REVERT: I 217 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7164 (mttm) REVERT: I 272 GLU cc_start: 0.8171 (pt0) cc_final: 0.7822 (mp0) REVERT: I 311 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8607 (tt) REVERT: J 43 ASP cc_start: 0.7986 (m-30) cc_final: 0.7769 (m-30) REVERT: J 308 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5838 (tm-30) REVERT: J 323 MET cc_start: 0.4036 (tpp) cc_final: 0.3646 (tpp) REVERT: J 387 ARG cc_start: 0.5619 (ptm-80) cc_final: 0.5098 (ptm-80) outliers start: 95 outliers final: 83 residues processed: 351 average time/residue: 0.1690 time to fit residues: 98.1717 Evaluate side-chains 346 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 257 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 209 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 342 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN J 202 ASN J 386 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113790 restraints weight = 44598.650| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.87 r_work: 0.3041 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29816 Z= 0.187 Angle : 0.778 14.530 40742 Z= 0.400 Chirality : 0.046 0.258 4503 Planarity : 0.005 0.074 5002 Dihedral : 14.588 177.945 4661 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.65 % Favored : 83.88 % Rotamer: Outliers : 3.22 % Allowed : 19.13 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 0.98 % 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: -2.96 (0.14), residues: 3400 helix: -0.74 (0.17), residues: 932 sheet: -0.63 (0.22), residues: 522 loop : -3.15 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 110 TYR 0.018 0.002 TYR E 275 PHE 0.033 0.002 PHE I 40 TRP 0.023 0.001 TRP J 142 HIS 0.026 0.001 HIS F 315 Details of bonding type rmsd covalent geometry : bond 0.00432 (29814) covalent geometry : angle 0.77804 (40742) hydrogen bonds : bond 0.03571 ( 753) hydrogen bonds : angle 5.00275 ( 2089) Misc. bond : bond 0.00214 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6377.53 seconds wall clock time: 110 minutes 7.52 seconds (6607.52 seconds total)