Starting phenix.real_space_refine on Mon Sep 14 07:46:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.map" model { file = "/net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5u0a_8478/09_2026/5u0a_8478.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.017 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 143 5.49 5 S 46 5.16 5 C 17670 2.51 5 N 5313 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28923 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1439 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 182} Chain breaks: 8 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3980 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 41, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2017 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "E" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "F" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "G" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "H" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2543 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1388 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "K" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1267 Classifications: {'RNAv2': 59} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1322 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1013 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "N" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1896 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 20, 'TRANS': 220} Chain breaks: 1 Chain: "O" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.20 Number of scatterers: 28923 At special positions: 0 Unit cell: (188.19, 131.61, 145.14, 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 46 16.00 P 143 15.00 O 5751 8.00 N 5313 7.00 C 17670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 32 sheets defined 45.9% alpha, 17.7% beta 28 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.630A pdb=" N GLY A 217 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.832A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 89 through 105 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.673A pdb=" N VAL C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.842A pdb=" N PHE C 123 " --> pdb=" O SER C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.986A pdb=" N GLU C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 142' Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 227 through 235 removed outlier: 3.567A pdb=" N SER C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.721A pdb=" N HIS C 343 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.078A pdb=" N SER C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 removed outlier: 4.517A pdb=" N ARG C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 446 Processing helix chain 'C' and resid 464 through 487 removed outlier: 3.773A pdb=" N HIS C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.609A pdb=" N VAL C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 522 through 534 Processing helix chain 'C' and resid 535 through 538 removed outlier: 3.721A pdb=" N SER C 538 " --> pdb=" O THR C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 248 through 266 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 355 through 368 removed outlier: 3.647A pdb=" N PHE D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.788A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.938A pdb=" N HIS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 144 removed outlier: 3.857A pdb=" N LYS E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE E 156 " --> pdb=" O PRO E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 248 through 266 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 309 through 329 removed outlier: 4.242A pdb=" N ARG E 313 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 350 " --> pdb=" O ALA E 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 350' Processing helix chain 'E' and resid 355 through 368 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.501A pdb=" N TRP F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.719A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 248 through 266 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU F 349 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 350 " --> pdb=" O ALA F 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 346 through 350' Processing helix chain 'F' and resid 355 through 368 Processing helix chain 'G' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.938A pdb=" N HIS G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 171 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 248 through 266 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG G 313 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 350 removed outlier: 3.587A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY G 350 " --> pdb=" O ALA G 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 346 through 350' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'H' and resid 39 through 56 removed outlier: 3.501A pdb=" N TRP H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 144 removed outlier: 3.857A pdb=" N LYS H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 248 through 266 Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG H 313 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.586A pdb=" N LEU H 349 " --> pdb=" O LEU H 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY H 350 " --> pdb=" O ALA H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 355 through 367 Processing helix chain 'I' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 93 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE I 156 " --> pdb=" O PRO I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 171 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 248 through 266 Processing helix chain 'I' and resid 296 through 301 Processing helix chain 'I' and resid 309 through 329 removed outlier: 4.243A pdb=" N ARG I 313 " --> pdb=" O GLY I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU I 349 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY I 350 " --> pdb=" O ALA I 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 346 through 350' Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'J' and resid 6 through 24 removed outlier: 4.033A pdb=" N VAL J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 33 removed outlier: 3.691A pdb=" N ARG J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 45 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 75 through 90 Processing helix chain 'J' and resid 92 through 98 removed outlier: 3.753A pdb=" N GLN J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 153 through 165 Processing helix chain 'J' and resid 168 through 186 removed outlier: 3.604A pdb=" N HIS J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Proline residue: J 177 - end of helix removed outlier: 4.013A pdb=" N ASP J 186 " --> pdb=" O TYR J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 Processing helix chain 'J' and resid 209 through 228 removed outlier: 3.554A pdb=" N ALA J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 24 removed outlier: 3.694A pdb=" N HIS L 9 " --> pdb=" O TYR L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 33 Processing helix chain 'L' and resid 45 through 51 Processing helix chain 'L' and resid 75 through 90 removed outlier: 4.089A pdb=" N VAL L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.650A pdb=" N GLN L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 Processing helix chain 'L' and resid 153 through 167 removed outlier: 3.588A pdb=" N GLN L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 167 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 186 removed outlier: 3.869A pdb=" N HIS L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG L 174 " --> pdb=" O ASP L 170 " (cutoff:3.500A) Proline residue: L 177 - end of helix Processing helix chain 'L' and resid 191 through 205 removed outlier: 3.881A pdb=" N GLY L 203 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS L 204 " --> pdb=" O ALA L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 229 removed outlier: 3.944A pdb=" N VAL L 209 " --> pdb=" O THR L 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 44 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.724A pdb=" N THR N 85 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 130 Processing helix chain 'N' and resid 157 through 164 removed outlier: 3.785A pdb=" N GLU N 161 " --> pdb=" O ASP N 157 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.302A pdb=" N TYR A 63 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.039A pdb=" N VAL A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.674A pdb=" N ILE C 29 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 56 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.559A pdb=" N LEU C 176 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 293 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 219 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 315 through 318 removed outlier: 3.515A pdb=" N ARG C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.291A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 192 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.164A pdb=" N SER D 227 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR D 14 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 5 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 283 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 336 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AB5, first strand: chain 'E' and resid 200 through 207 Processing sheet with id=AB6, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.161A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.161A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 59 through 62 Processing sheet with id=AB9, first strand: chain 'F' and resid 200 through 206 Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'G' and resid 200 through 205 Processing sheet with id=AC5, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 62 Processing sheet with id=AC8, first strand: chain 'H' and resid 200 through 207 Processing sheet with id=AC9, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY I 229 " --> pdb=" O LEU I 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 59 through 62 Processing sheet with id=AD3, first strand: chain 'N' and resid 150 through 152 removed outlier: 5.274A pdb=" N VAL N 150 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG N 7 " --> pdb=" O VAL N 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG N 152 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL N 112 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG N 62 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR N 60 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP N 183 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ARG N 65 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 13.805A pdb=" N LEU N 181 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG N 213 " --> pdb=" O PRO N 204 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER N 215 " --> pdb=" O ASP N 202 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N 200 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'N' and resid 12 through 13 1333 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6173 1.32 - 1.45: 8270 1.45 - 1.58: 15021 1.58 - 1.71: 268 1.71 - 1.84: 80 Bond restraints: 29812 Sorted by residual: bond pdb=" C1' DC O 43 " pdb=" N1 DC O 43 " ideal model delta sigma weight residual 1.468 1.565 -0.097 1.40e-02 5.10e+03 4.83e+01 bond pdb=" C1' DT O 35 " pdb=" N1 DT O 35 " ideal model delta sigma weight residual 1.468 1.558 -0.090 1.40e-02 5.10e+03 4.12e+01 bond pdb=" C1' DC O 31 " pdb=" N1 DC O 31 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" C1' DT O 33 " pdb=" N1 DT O 33 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" C1' DC O 39 " pdb=" N1 DC O 39 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.12e+01 ... (remaining 29807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.85: 41079 9.85 - 19.69: 40 19.69 - 29.54: 0 29.54 - 39.39: 0 39.39 - 49.23: 1 Bond angle restraints: 41120 Sorted by residual: angle pdb=" C HIS A 185 " pdb=" N PRO A 186 " pdb=" CD PRO A 186 " ideal model delta sigma weight residual 125.00 75.77 49.23 4.10e+00 5.95e-02 1.44e+02 angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 112.68 97.58 15.10 1.26e+00 6.30e-01 1.44e+02 angle pdb=" N TRP C 163 " pdb=" CA TRP C 163 " pdb=" C TRP C 163 " ideal model delta sigma weight residual 111.28 123.18 -11.90 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ARG A 123 " pdb=" CA ARG A 123 " pdb=" C ARG A 123 " ideal model delta sigma weight residual 110.59 96.14 14.45 1.45e+00 4.76e-01 9.93e+01 angle pdb=" N ILE C 236 " pdb=" CA ILE C 236 " pdb=" C ILE C 236 " ideal model delta sigma weight residual 107.76 116.98 -9.22 1.01e+00 9.80e-01 8.33e+01 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 16572 32.17 - 64.34: 941 64.34 - 96.51: 44 96.51 - 128.68: 0 128.68 - 160.85: 2 Dihedral angle restraints: 17559 sinusoidal: 7904 harmonic: 9655 Sorted by residual: dihedral pdb=" C4' A K 54 " pdb=" C3' A K 54 " pdb=" C2' A K 54 " pdb=" C1' A K 54 " ideal model delta sinusoidal sigma weight residual 36.34 -39.79 76.13 1 3.10e+00 1.04e-01 7.60e+02 dihedral pdb=" C4' C K 9 " pdb=" C3' C K 9 " pdb=" C2' C K 9 " pdb=" C1' C K 9 " ideal model delta sinusoidal sigma weight residual 36.34 -39.46 75.81 1 3.10e+00 1.04e-01 7.54e+02 dihedral pdb=" C4' G K 45 " pdb=" C3' G K 45 " pdb=" C2' G K 45 " pdb=" C1' G K 45 " ideal model delta sinusoidal sigma weight residual 36.35 -38.71 75.06 1 3.10e+00 1.04e-01 7.41e+02 ... (remaining 17556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4304 0.149 - 0.298: 321 0.298 - 0.448: 27 0.448 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 4655 Sorted by residual: chirality pdb=" CG LEU N 138 " pdb=" CB LEU N 138 " pdb=" CD1 LEU N 138 " pdb=" CD2 LEU N 138 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CB THR D 193 " pdb=" CA THR D 193 " pdb=" OG1 THR D 193 " pdb=" CG2 THR D 193 " both_signs ideal model delta sigma weight residual False 2.55 1.99 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C1' DA M 50 " pdb=" O4' DA M 50 " pdb=" C2' DA M 50 " pdb=" N9 DA M 50 " both_signs ideal model delta sigma weight residual False 2.43 1.93 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 4652 not shown) Planarity restraints: 4869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 185 " -0.156 5.00e-02 4.00e+02 2.33e-01 8.66e+01 pdb=" N PRO A 186 " 0.398 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " -0.167 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 427 " 0.034 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" CD GLU C 427 " -0.119 2.00e-02 2.50e+03 pdb=" OE1 GLU C 427 " 0.042 2.00e-02 2.50e+03 pdb=" OE2 GLU C 427 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.006 2.00e-02 2.50e+03 3.67e-02 3.37e+01 pdb=" CG TRP C 390 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.003 2.00e-02 2.50e+03 ... (remaining 4866 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 94 2.31 - 2.96: 14742 2.96 - 3.61: 43232 3.61 - 4.25: 69502 4.25 - 4.90: 116165 Nonbonded interactions: 243735 Sorted by model distance: nonbonded pdb=" NE2 GLN A 122 " pdb=" N1 A K 44 " model vdw 1.667 3.200 nonbonded pdb=" OE1 GLN A 122 " pdb=" C5 A K 44 " model vdw 1.818 3.260 nonbonded pdb=" O ASP A 169 " pdb=" O ARG A 184 " model vdw 1.858 3.040 nonbonded pdb=" O GLN J 98 " pdb=" NE2 GLN J 98 " model vdw 1.876 3.120 nonbonded pdb=" NH2 ARG A 184 " pdb=" OP1 C K 46 " model vdw 1.926 3.120 ... (remaining 243730 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 'E' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'F' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'G' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'H' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 5 through 35 or resid 44 through 57 or resid 75 through 13 \ 5 or resid 137 through 215 or (resid 216 and (name N or name CA or name C or nam \ e O or name CB )) or resid 217 through 229)) selection = (chain 'L' and resid 5 through 229) } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.260 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 0.013 0.151 29812 Z= 0.633 Angle : 1.394 49.234 41120 Z= 0.812 Chirality : 0.085 0.746 4655 Planarity : 0.008 0.233 4869 Dihedral : 16.865 160.852 11305 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.65 % Favored : 94.80 % Rotamer: Outliers : 5.48 % Allowed : 6.64 % Favored : 87.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.12), residues: 3269 helix: -1.73 (0.11), residues: 1356 sheet: -2.28 (0.19), residues: 490 loop : -1.59 (0.14), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG A 113 TYR 0.085 0.004 TYR C 315 PHE 0.080 0.004 PHE E 226 TRP 0.079 0.006 TRP C 390 HIS 0.024 0.004 HIS H 216 Details of bonding type rmsd/Z covalent geometry : bond 0.01261 / 0.63 (29812) covalent geometry : angle 1.39419 / 0.81 (41120) hydrogen bonds : bond 0.15781 / 10.65 ( 1357) hydrogen bonds : angle 8.57061 / 5.98 ( 3858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 730 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.1497 (mtt) cc_final: 0.0768 (mtm) REVERT: A 112 LYS cc_start: 0.3622 (OUTLIER) cc_final: 0.2391 (tttt) REVERT: C 51 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8114 (t) REVERT: C 106 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5857 (ptm-80) REVERT: C 118 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7702 (t0) REVERT: C 169 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.6189 (m90) REVERT: C 215 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8321 (pp) REVERT: C 336 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6769 (ttt180) REVERT: C 343 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.4987 (t-90) REVERT: C 357 ASN cc_start: 0.7696 (m-40) cc_final: 0.7479 (m110) REVERT: C 424 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8632 (mmmt) REVERT: C 434 GLU cc_start: 0.6339 (pp20) cc_final: 0.5745 (pp20) REVERT: C 522 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (mtm180) REVERT: D 20 ASP cc_start: 0.8280 (m-30) cc_final: 0.8009 (m-30) REVERT: D 50 GLU cc_start: 0.7878 (tp30) cc_final: 0.7602 (tp30) REVERT: D 341 GLU cc_start: 0.5122 (OUTLIER) cc_final: 0.4919 (pp20) REVERT: D 354 ASP cc_start: 0.7225 (m-30) cc_final: 0.6917 (p0) REVERT: E 21 ASP cc_start: 0.8093 (t70) cc_final: 0.7543 (p0) REVERT: E 148 LYS cc_start: 0.8241 (mttp) cc_final: 0.7474 (mmmm) REVERT: E 266 THR cc_start: 0.9017 (t) cc_final: 0.8732 (p) REVERT: F 5 ASP cc_start: 0.8052 (p0) cc_final: 0.7834 (p0) REVERT: F 22 LEU cc_start: 0.8488 (mt) cc_final: 0.8253 (mt) REVERT: F 113 THR cc_start: 0.8759 (p) cc_final: 0.8519 (t) REVERT: F 119 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8313 (pp) REVERT: G 154 ASP cc_start: 0.7811 (t0) cc_final: 0.7357 (t0) REVERT: G 221 MET cc_start: 0.8833 (mtp) cc_final: 0.8281 (mtp) REVERT: H 155 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7498 (mtp180) REVERT: H 208 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: H 234 TYR cc_start: 0.8959 (t80) cc_final: 0.8624 (t80) REVERT: H 253 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.6145 (mmt-90) REVERT: I 147 PRO cc_start: 0.7757 (Cg_endo) cc_final: 0.7482 (Cg_exo) REVERT: J 157 THR cc_start: 0.9367 (t) cc_final: 0.9031 (p) REVERT: J 211 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6924 (mtp85) REVERT: L 8 GLN cc_start: 0.7226 (mt0) cc_final: 0.6751 (mt0) REVERT: L 18 SER cc_start: 0.7752 (t) cc_final: 0.7548 (p) REVERT: L 182 TYR cc_start: 0.8434 (t80) cc_final: 0.8230 (t80) REVERT: L 191 ASP cc_start: 0.8586 (t0) cc_final: 0.8305 (t0) REVERT: N 13 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: N 65 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7402 (ttp-170) REVERT: N 110 ASP cc_start: 0.6775 (t70) cc_final: 0.6373 (t70) REVERT: N 137 TYR cc_start: 0.8150 (p90) cc_final: 0.7901 (p90) REVERT: N 205 LEU cc_start: 0.8330 (mp) cc_final: 0.7900 (mp) REVERT: N 206 SER cc_start: 0.8069 (t) cc_final: 0.7487 (t) REVERT: N 244 THR cc_start: 0.8417 (m) cc_final: 0.8104 (p) outliers start: 146 outliers final: 48 residues processed: 835 average time/residue: 0.2446 time to fit residues: 300.2337 Evaluate side-chains 445 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 368 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 18 HIS Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 231 VAL Chi-restraints excluded: chain N residue 242 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS A 166 GLN C 100 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 236 ASN E 18 ASN E 89 GLN E 134 HIS E 195 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 89 GLN F 195 HIS F 216 HIS ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 195 HIS G 273 ASN H 89 GLN ** H 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 HIS H 214 ASN H 225 GLN I 16 ASN I 18 ASN I 89 GLN I 134 HIS I 195 HIS L 145 GLN L 167 GLN L 173 HIS L 175 HIS L 208 HIS ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130829 restraints weight = 40361.680| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.85 r_work: 0.3352 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29812 Z= 0.200 Angle : 0.990 23.716 41120 Z= 0.465 Chirality : 0.072 1.402 4655 Planarity : 0.007 0.183 4869 Dihedral : 17.767 156.119 5457 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 4.39 % Allowed : 12.16 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 3269 helix: -0.16 (0.13), residues: 1371 sheet: -1.69 (0.21), residues: 457 loop : -1.18 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 54 TYR 0.017 0.002 TYR C 473 PHE 0.022 0.002 PHE C 379 TRP 0.022 0.002 TRP F 78 HIS 0.011 0.002 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (29812) covalent geometry : angle 0.99016 / 0.47 (41120) hydrogen bonds : bond 0.05730 / 3.92 ( 1357) hydrogen bonds : angle 5.79899 / 4.01 ( 3858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 515 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.2632 (mtt) cc_final: 0.1928 (mtm) REVERT: A 184 ARG cc_start: 0.2630 (OUTLIER) cc_final: 0.2379 (mpt180) REVERT: C 24 ILE cc_start: 0.7765 (mp) cc_final: 0.7518 (pt) REVERT: C 33 ARG cc_start: 0.7537 (mtp-110) cc_final: 0.7334 (mtm110) REVERT: C 118 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7925 (t0) REVERT: C 169 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.6277 (m90) REVERT: C 301 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7491 (mmp-170) REVERT: C 343 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.4933 (t-90) REVERT: C 424 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8706 (mmmt) REVERT: C 434 GLU cc_start: 0.7362 (pp20) cc_final: 0.6742 (pp20) REVERT: C 438 LYS cc_start: 0.9122 (tttp) cc_final: 0.8600 (ttmt) REVERT: C 441 TRP cc_start: 0.8280 (t60) cc_final: 0.7996 (t-100) REVERT: C 524 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7231 (ptm-80) REVERT: D 20 ASP cc_start: 0.8307 (m-30) cc_final: 0.8059 (m-30) REVERT: D 296 PHE cc_start: 0.9185 (m-10) cc_final: 0.8959 (m-10) REVERT: D 341 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5631 (pp20) REVERT: D 354 ASP cc_start: 0.7863 (m-30) cc_final: 0.7481 (p0) REVERT: E 148 LYS cc_start: 0.8329 (mttp) cc_final: 0.8102 (mmmm) REVERT: E 266 THR cc_start: 0.9181 (t) cc_final: 0.8927 (p) REVERT: E 312 LEU cc_start: 0.8028 (tp) cc_final: 0.7737 (tp) REVERT: E 363 MET cc_start: 0.8196 (mmt) cc_final: 0.7740 (mmt) REVERT: F 5 ASP cc_start: 0.8092 (p0) cc_final: 0.7708 (p0) REVERT: F 75 GLU cc_start: 0.7869 (pp20) cc_final: 0.7414 (tt0) REVERT: F 97 LYS cc_start: 0.7031 (mptt) cc_final: 0.6416 (ttpt) REVERT: F 119 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8482 (pp) REVERT: F 301 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7966 (tm-30) REVERT: G 5 ASP cc_start: 0.8321 (p0) cc_final: 0.7994 (p0) REVERT: G 43 TRP cc_start: 0.9282 (OUTLIER) cc_final: 0.8740 (t-100) REVERT: G 101 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (ttpt) REVERT: G 154 ASP cc_start: 0.8426 (t0) cc_final: 0.8151 (t0) REVERT: G 221 MET cc_start: 0.8692 (mtp) cc_final: 0.8367 (mtp) REVERT: H 158 GLU cc_start: 0.8055 (tp30) cc_final: 0.7669 (pt0) REVERT: H 208 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: H 221 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8401 (ptp) REVERT: H 253 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.6390 (mmt-90) REVERT: H 363 MET cc_start: 0.8968 (mmt) cc_final: 0.8426 (mmt) REVERT: I 310 TYR cc_start: 0.6783 (m-80) cc_final: 0.6280 (m-10) REVERT: J 211 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7468 (mtp85) REVERT: L 8 GLN cc_start: 0.7388 (mt0) cc_final: 0.6920 (mt0) REVERT: N 110 ASP cc_start: 0.7356 (t70) cc_final: 0.6959 (t0) REVERT: N 171 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6992 (ttm110) REVERT: N 174 GLU cc_start: 0.7176 (mp0) cc_final: 0.6851 (mm-30) REVERT: N 206 SER cc_start: 0.8261 (t) cc_final: 0.7872 (p) REVERT: N 208 ASP cc_start: 0.7919 (t0) cc_final: 0.7380 (p0) REVERT: N 225 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7845 (mm-30) outliers start: 117 outliers final: 52 residues processed: 596 average time/residue: 0.2117 time to fit residues: 193.8460 Evaluate side-chains 433 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 368 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 181 optimal weight: 0.0030 chunk 190 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS A 122 GLN C 134 GLN C 357 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN D 245 ASN E 89 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN H 134 HIS H 225 GLN H 273 ASN J 9 HIS J 23 ASN J 91 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** 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 = 0.3974 r_free = 0.3974 target = 0.166080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127551 restraints weight = 40179.923| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.89 r_work: 0.3289 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 29812 Z= 0.170 Angle : 0.782 14.632 41120 Z= 0.381 Chirality : 0.058 0.704 4655 Planarity : 0.006 0.155 4869 Dihedral : 17.527 153.688 5363 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.51 % Rotamer: Outliers : 4.50 % Allowed : 14.07 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3269 helix: 0.49 (0.13), residues: 1367 sheet: -1.49 (0.21), residues: 490 loop : -0.93 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 226 TYR 0.021 0.002 TYR H 30 PHE 0.039 0.002 PHE C 379 TRP 0.016 0.001 TRP C 401 HIS 0.010 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (29812) covalent geometry : angle 0.78198 / 0.38 (41120) hydrogen bonds : bond 0.04903 / 3.39 ( 1357) hydrogen bonds : angle 5.17544 / 3.57 ( 3858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 414 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.1611 (mtt) cc_final: 0.1310 (mtm) REVERT: A 112 LYS cc_start: -0.1384 (OUTLIER) cc_final: -0.1770 (tptt) REVERT: C 21 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7674 (t0) REVERT: C 24 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7548 (pt) REVERT: C 42 LEU cc_start: 0.7822 (pp) cc_final: 0.7597 (pp) REVERT: C 97 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7410 (mtt180) REVERT: C 118 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7953 (t0) REVERT: C 169 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.6294 (m90) REVERT: C 200 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.4181 (pmt-80) REVERT: C 343 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.5117 (t-90) REVERT: C 357 ASN cc_start: 0.7611 (m-40) cc_final: 0.7160 (m-40) REVERT: C 434 GLU cc_start: 0.7134 (pp20) cc_final: 0.6899 (pp20) REVERT: C 438 LYS cc_start: 0.9173 (tttp) cc_final: 0.8569 (ttmt) REVERT: C 445 ASN cc_start: 0.7278 (m110) cc_final: 0.6429 (t0) REVERT: D 20 ASP cc_start: 0.8052 (m-30) cc_final: 0.7773 (m-30) REVERT: D 296 PHE cc_start: 0.9249 (m-10) cc_final: 0.8977 (m-10) REVERT: D 341 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5823 (pp20) REVERT: D 354 ASP cc_start: 0.7746 (m-30) cc_final: 0.7423 (p0) REVERT: E 71 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7578 (ptpp) REVERT: E 148 LYS cc_start: 0.8298 (mttp) cc_final: 0.8086 (mmmm) REVERT: E 266 THR cc_start: 0.9146 (t) cc_final: 0.8924 (p) REVERT: E 312 LEU cc_start: 0.7929 (tp) cc_final: 0.7728 (tp) REVERT: E 316 GLN cc_start: 0.7825 (mt0) cc_final: 0.7397 (mt0) REVERT: E 363 MET cc_start: 0.8168 (mmt) cc_final: 0.7605 (mmt) REVERT: F 75 GLU cc_start: 0.8009 (pp20) cc_final: 0.7390 (tt0) REVERT: F 97 LYS cc_start: 0.6964 (mptt) cc_final: 0.6428 (ttpt) REVERT: F 125 ASP cc_start: 0.7084 (t0) cc_final: 0.6720 (t0) REVERT: F 208 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: F 258 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: F 278 MET cc_start: 0.8889 (mmm) cc_final: 0.8181 (mmt) REVERT: G 43 TRP cc_start: 0.9336 (OUTLIER) cc_final: 0.8815 (t-100) REVERT: G 91 VAL cc_start: 0.8513 (t) cc_final: 0.8015 (m) REVERT: G 154 ASP cc_start: 0.8216 (t0) cc_final: 0.7972 (t0) REVERT: G 173 MET cc_start: 0.8890 (ttt) cc_final: 0.8396 (ttt) REVERT: G 227 SER cc_start: 0.9039 (t) cc_final: 0.8600 (m) REVERT: H 119 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9047 (pp) REVERT: H 208 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: H 221 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8336 (ptp) REVERT: H 253 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.6399 (mmt-90) REVERT: I 193 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8592 (p) REVERT: I 250 GLN cc_start: 0.7826 (mm110) cc_final: 0.7451 (tp-100) REVERT: I 288 VAL cc_start: 0.7762 (t) cc_final: 0.7395 (m) REVERT: I 289 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.6219 (ptm160) REVERT: L 8 GLN cc_start: 0.7334 (mt0) cc_final: 0.6844 (mt0) REVERT: L 215 GLN cc_start: 0.8452 (mt0) cc_final: 0.8205 (mt0) REVERT: N 65 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8122 (ttp-170) REVERT: N 110 ASP cc_start: 0.7300 (t70) cc_final: 0.6956 (t70) REVERT: N 137 TYR cc_start: 0.8279 (p90) cc_final: 0.7979 (p90) outliers start: 120 outliers final: 57 residues processed: 504 average time/residue: 0.2188 time to fit residues: 170.3954 Evaluate side-chains 431 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 356 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 48 optimal weight: 0.6980 chunk 265 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN G 225 GLN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS J 23 ASN L 215 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123779 restraints weight = 39847.579| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.89 r_work: 0.3226 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29812 Z= 0.189 Angle : 0.751 14.895 41120 Z= 0.371 Chirality : 0.058 0.739 4655 Planarity : 0.006 0.136 4869 Dihedral : 17.222 154.974 5337 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 4.80 % Allowed : 14.97 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3269 helix: 0.82 (0.14), residues: 1374 sheet: -1.27 (0.21), residues: 490 loop : -0.83 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 241 TYR 0.024 0.002 TYR F 14 PHE 0.026 0.002 PHE C 379 TRP 0.017 0.002 TRP C 390 HIS 0.009 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (29812) covalent geometry : angle 0.75096 / 0.37 (41120) hydrogen bonds : bond 0.04605 / 3.21 ( 1357) hydrogen bonds : angle 4.95106 / 3.43 ( 3858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 376 time to evaluate : 1.277 Fit side-chains REVERT: A 86 MET cc_start: 0.1941 (mtt) cc_final: 0.1412 (mtm) REVERT: A 112 LYS cc_start: -0.1353 (OUTLIER) cc_final: -0.2069 (tptt) REVERT: C 21 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7687 (t0) REVERT: C 24 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7645 (pt) REVERT: C 42 LEU cc_start: 0.7971 (pp) cc_final: 0.7648 (pp) REVERT: C 46 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7942 (t70) REVERT: C 56 ASP cc_start: 0.6053 (t0) cc_final: 0.5848 (t70) REVERT: C 58 GLU cc_start: 0.7636 (tt0) cc_final: 0.7386 (tt0) REVERT: C 76 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6714 (t) REVERT: C 97 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7436 (mtt180) REVERT: C 98 ARG cc_start: 0.8165 (ttt90) cc_final: 0.7561 (ttt-90) REVERT: C 118 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8094 (t70) REVERT: C 169 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.6476 (m90) REVERT: C 177 ASP cc_start: 0.7753 (m-30) cc_final: 0.7514 (m-30) REVERT: C 180 GLU cc_start: 0.8132 (tt0) cc_final: 0.7648 (mt-10) REVERT: C 200 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.4568 (pmt-80) REVERT: C 215 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8482 (pp) REVERT: C 343 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.5302 (t-90) REVERT: C 357 ASN cc_start: 0.7628 (m-40) cc_final: 0.7254 (m-40) REVERT: C 363 GLN cc_start: 0.5835 (tm-30) cc_final: 0.3986 (tm-30) REVERT: C 434 GLU cc_start: 0.7175 (pp20) cc_final: 0.6967 (pp20) REVERT: C 438 LYS cc_start: 0.9120 (tttp) cc_final: 0.8582 (ttmt) REVERT: C 445 ASN cc_start: 0.7217 (m110) cc_final: 0.6537 (t0) REVERT: C 524 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7236 (ptm-80) REVERT: D 20 ASP cc_start: 0.8112 (m-30) cc_final: 0.7848 (m-30) REVERT: D 50 GLU cc_start: 0.8273 (tp30) cc_final: 0.7975 (tp30) REVERT: D 234 TYR cc_start: 0.8894 (t80) cc_final: 0.8621 (t80) REVERT: D 354 ASP cc_start: 0.7932 (m-30) cc_final: 0.7672 (p0) REVERT: E 266 THR cc_start: 0.9268 (t) cc_final: 0.9027 (p) REVERT: E 316 GLN cc_start: 0.7900 (mt0) cc_final: 0.7486 (mt0) REVERT: E 363 MET cc_start: 0.8386 (mmp) cc_final: 0.8083 (mmt) REVERT: F 14 TYR cc_start: 0.8755 (t80) cc_final: 0.8536 (t80) REVERT: F 97 LYS cc_start: 0.7000 (mptt) cc_final: 0.6428 (ttpt) REVERT: F 208 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: F 258 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: F 278 MET cc_start: 0.9003 (mmm) cc_final: 0.8332 (mmt) REVERT: G 7 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8709 (m-70) REVERT: G 43 TRP cc_start: 0.9372 (OUTLIER) cc_final: 0.8812 (t-100) REVERT: G 91 VAL cc_start: 0.8641 (t) cc_final: 0.8131 (m) REVERT: G 154 ASP cc_start: 0.8169 (t0) cc_final: 0.7954 (t0) REVERT: G 173 MET cc_start: 0.8988 (ttt) cc_final: 0.8499 (ttt) REVERT: G 225 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8611 (mp10) REVERT: H 119 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9078 (pp) REVERT: H 208 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: H 253 ARG cc_start: 0.8429 (ttt-90) cc_final: 0.6432 (mmt-90) REVERT: H 341 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: H 363 MET cc_start: 0.9062 (mmt) cc_final: 0.8313 (mmt) REVERT: I 188 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.7532 (t80) REVERT: I 193 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8628 (p) REVERT: I 250 GLN cc_start: 0.8048 (mm110) cc_final: 0.7806 (tp40) REVERT: I 289 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.6637 (ptm160) REVERT: L 8 GLN cc_start: 0.7504 (mt0) cc_final: 0.7049 (mt0) REVERT: L 88 MET cc_start: 0.8782 (mtp) cc_final: 0.8485 (ttm) REVERT: N 110 ASP cc_start: 0.7378 (t70) cc_final: 0.6929 (t0) REVERT: N 206 SER cc_start: 0.8386 (t) cc_final: 0.8043 (p) outliers start: 128 outliers final: 67 residues processed: 469 average time/residue: 0.2092 time to fit residues: 154.5075 Evaluate side-chains 423 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 334 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 286 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 89 GLN E 273 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121111 restraints weight = 39868.476| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.81 r_work: 0.3186 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29812 Z= 0.194 Angle : 0.730 13.359 41120 Z= 0.361 Chirality : 0.056 0.644 4655 Planarity : 0.005 0.068 4869 Dihedral : 17.172 157.501 5326 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 4.65 % Allowed : 16.40 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3269 helix: 0.98 (0.14), residues: 1373 sheet: -1.27 (0.21), residues: 479 loop : -0.80 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 432 TYR 0.026 0.002 TYR N 137 PHE 0.019 0.002 PHE C 379 TRP 0.021 0.001 TRP C 390 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (29812) covalent geometry : angle 0.73045 / 0.36 (41120) hydrogen bonds : bond 0.04510 / 3.14 ( 1357) hydrogen bonds : angle 4.90991 / 3.39 ( 3858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 353 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.2292 (mtt) cc_final: 0.1550 (mtm) REVERT: A 112 LYS cc_start: -0.1392 (OUTLIER) cc_final: -0.1775 (tptt) REVERT: C 21 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7918 (t0) REVERT: C 24 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7672 (pt) REVERT: C 56 ASP cc_start: 0.6346 (t0) cc_final: 0.6016 (t70) REVERT: C 76 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.6989 (t) REVERT: C 97 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7574 (mtt180) REVERT: C 118 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8300 (t70) REVERT: C 196 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7531 (mpt) REVERT: C 200 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.4542 (pmt-80) REVERT: C 215 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8522 (pp) REVERT: C 357 ASN cc_start: 0.7837 (m-40) cc_final: 0.7519 (m-40) REVERT: C 438 LYS cc_start: 0.9146 (tttp) cc_final: 0.8672 (ttmt) REVERT: C 445 ASN cc_start: 0.7134 (m110) cc_final: 0.6301 (t0) REVERT: C 524 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7299 (ptm-80) REVERT: D 7 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8747 (m-70) REVERT: D 20 ASP cc_start: 0.8372 (m-30) cc_final: 0.8154 (m-30) REVERT: D 50 GLU cc_start: 0.8551 (tp30) cc_final: 0.8131 (tp30) REVERT: D 354 ASP cc_start: 0.8259 (m-30) cc_final: 0.7878 (p0) REVERT: E 188 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: E 266 THR cc_start: 0.9329 (t) cc_final: 0.9091 (p) REVERT: E 316 GLN cc_start: 0.8161 (mt0) cc_final: 0.7760 (mt0) REVERT: E 361 ASP cc_start: 0.7670 (m-30) cc_final: 0.7442 (m-30) REVERT: E 363 MET cc_start: 0.8574 (mmp) cc_final: 0.8229 (mmt) REVERT: F 93 SER cc_start: 0.8190 (p) cc_final: 0.7727 (t) REVERT: F 97 LYS cc_start: 0.7239 (mptt) cc_final: 0.6612 (ttpt) REVERT: F 208 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: F 278 MET cc_start: 0.9175 (mmm) cc_final: 0.8512 (mmt) REVERT: G 7 HIS cc_start: 0.9032 (OUTLIER) cc_final: 0.8708 (m-70) REVERT: G 43 TRP cc_start: 0.9435 (OUTLIER) cc_final: 0.8932 (t-100) REVERT: G 154 ASP cc_start: 0.8509 (t0) cc_final: 0.8219 (t0) REVERT: G 173 MET cc_start: 0.9107 (ttt) cc_final: 0.8651 (ttt) REVERT: H 119 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9171 (pp) REVERT: H 208 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: H 253 ARG cc_start: 0.8603 (ttt-90) cc_final: 0.6460 (mmt-90) REVERT: H 363 MET cc_start: 0.9168 (mmt) cc_final: 0.8337 (mmt) REVERT: I 126 GLU cc_start: 0.8310 (tt0) cc_final: 0.8022 (mm-30) REVERT: I 188 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7687 (t80) REVERT: I 193 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8736 (p) REVERT: I 250 GLN cc_start: 0.8263 (mm110) cc_final: 0.7893 (tp-100) REVERT: I 289 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.7051 (ptm160) REVERT: L 8 GLN cc_start: 0.7694 (mt0) cc_final: 0.7370 (mt0) REVERT: L 88 MET cc_start: 0.8921 (mtp) cc_final: 0.8634 (ttm) REVERT: N 97 LYS cc_start: 0.7872 (tttt) cc_final: 0.7632 (tptm) REVERT: N 110 ASP cc_start: 0.7864 (t70) cc_final: 0.7438 (t0) REVERT: N 160 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7913 (mtp180) REVERT: N 206 SER cc_start: 0.8562 (t) cc_final: 0.8206 (p) outliers start: 124 outliers final: 69 residues processed: 445 average time/residue: 0.2121 time to fit residues: 148.7653 Evaluate side-chains 413 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 325 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN D 225 GLN F 49 HIS ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123109 restraints weight = 39764.774| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.82 r_work: 0.3248 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29812 Z= 0.137 Angle : 0.683 12.371 41120 Z= 0.336 Chirality : 0.052 0.647 4655 Planarity : 0.005 0.060 4869 Dihedral : 17.075 157.763 5320 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.78 % Favored : 97.09 % Rotamer: Outliers : 3.90 % Allowed : 17.75 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3269 helix: 1.18 (0.14), residues: 1374 sheet: -1.14 (0.21), residues: 478 loop : -0.68 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 181 TYR 0.018 0.001 TYR N 137 PHE 0.014 0.001 PHE C 379 TRP 0.018 0.001 TRP C 390 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (29812) covalent geometry : angle 0.68287 / 0.34 (41120) hydrogen bonds : bond 0.04183 / 2.93 ( 1357) hydrogen bonds : angle 4.73563 / 3.28 ( 3858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 361 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.2145 (mtt) cc_final: 0.1571 (mtm) REVERT: C 24 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7613 (pt) REVERT: C 56 ASP cc_start: 0.6343 (t0) cc_final: 0.6118 (t70) REVERT: C 76 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6867 (t) REVERT: C 196 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7090 (mpt) REVERT: C 200 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.4837 (pmt-80) REVERT: C 215 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8541 (pp) REVERT: C 357 ASN cc_start: 0.7619 (m-40) cc_final: 0.7336 (m-40) REVERT: C 438 LYS cc_start: 0.9026 (tttp) cc_final: 0.8613 (ttmt) REVERT: C 445 ASN cc_start: 0.7113 (m110) cc_final: 0.6373 (t0) REVERT: C 524 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7259 (ptm-80) REVERT: D 7 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8614 (m-70) REVERT: D 20 ASP cc_start: 0.8231 (m-30) cc_final: 0.7985 (m-30) REVERT: D 50 GLU cc_start: 0.8391 (tp30) cc_final: 0.7983 (tp30) REVERT: D 354 ASP cc_start: 0.8183 (m-30) cc_final: 0.7802 (p0) REVERT: E 124 ILE cc_start: 0.8293 (tt) cc_final: 0.8027 (mt) REVERT: E 188 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: E 266 THR cc_start: 0.9311 (t) cc_final: 0.9105 (p) REVERT: E 316 GLN cc_start: 0.8067 (mt0) cc_final: 0.7675 (mt0) REVERT: E 361 ASP cc_start: 0.7579 (m-30) cc_final: 0.7332 (m-30) REVERT: F 93 SER cc_start: 0.8177 (p) cc_final: 0.7806 (t) REVERT: F 97 LYS cc_start: 0.7246 (mptt) cc_final: 0.6670 (ttpt) REVERT: F 208 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: F 278 MET cc_start: 0.9177 (mmm) cc_final: 0.8500 (mmt) REVERT: G 43 TRP cc_start: 0.9404 (OUTLIER) cc_final: 0.8956 (t-100) REVERT: G 140 LYS cc_start: 0.8249 (mmtm) cc_final: 0.8041 (ttpt) REVERT: G 154 ASP cc_start: 0.8486 (t0) cc_final: 0.8204 (t0) REVERT: G 173 MET cc_start: 0.9046 (ttt) cc_final: 0.8612 (ttt) REVERT: H 7 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.9057 (m90) REVERT: H 119 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9130 (pp) REVERT: H 208 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: H 253 ARG cc_start: 0.8567 (ttt-90) cc_final: 0.6460 (mmt-90) REVERT: H 363 MET cc_start: 0.9132 (mmt) cc_final: 0.8235 (mmt) REVERT: I 188 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7717 (t80) REVERT: I 250 GLN cc_start: 0.8202 (mm110) cc_final: 0.7882 (tp-100) REVERT: I 289 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7088 (ptm160) REVERT: L 8 GLN cc_start: 0.7704 (mt0) cc_final: 0.7257 (mt0) REVERT: L 88 MET cc_start: 0.8863 (mtp) cc_final: 0.8580 (ttm) REVERT: N 69 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8183 (ttm-80) REVERT: N 71 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8799 (t) REVERT: N 110 ASP cc_start: 0.7808 (t70) cc_final: 0.7344 (t0) REVERT: N 160 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7981 (mtp180) REVERT: N 206 SER cc_start: 0.8509 (t) cc_final: 0.8170 (p) outliers start: 104 outliers final: 65 residues processed: 437 average time/residue: 0.1941 time to fit residues: 133.3945 Evaluate side-chains 411 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 330 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 66 optimal weight: 7.9990 chunk 138 optimal weight: 0.0670 chunk 339 optimal weight: 40.0000 chunk 235 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 276 optimal weight: 0.7980 chunk 309 optimal weight: 50.0000 chunk 120 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 225 GLN H 18 ASN I 49 HIS J 91 GLN L 153 ASN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123068 restraints weight = 39981.837| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.91 r_work: 0.3254 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29812 Z= 0.132 Angle : 0.662 11.570 41120 Z= 0.325 Chirality : 0.050 0.623 4655 Planarity : 0.005 0.060 4869 Dihedral : 16.987 159.181 5318 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 4.02 % Allowed : 17.97 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3269 helix: 1.34 (0.14), residues: 1380 sheet: -1.02 (0.21), residues: 469 loop : -0.63 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 211 TYR 0.023 0.001 TYR N 137 PHE 0.015 0.001 PHE G 226 TRP 0.018 0.001 TRP C 390 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (29812) covalent geometry : angle 0.66163 / 0.33 (41120) hydrogen bonds : bond 0.04035 / 2.83 ( 1357) hydrogen bonds : angle 4.62338 / 3.21 ( 3858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 354 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.2100 (mtt) cc_final: 0.1564 (mtm) REVERT: C 22 VAL cc_start: 0.8382 (t) cc_final: 0.8130 (p) REVERT: C 24 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7614 (pt) REVERT: C 76 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6873 (t) REVERT: C 132 TRP cc_start: 0.8083 (t-100) cc_final: 0.7825 (t-100) REVERT: C 196 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7246 (mpt) REVERT: C 200 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.4453 (pmt-80) REVERT: C 215 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8569 (pp) REVERT: C 357 ASN cc_start: 0.7665 (m-40) cc_final: 0.7361 (m-40) REVERT: C 438 LYS cc_start: 0.9031 (tttp) cc_final: 0.8647 (ttmt) REVERT: C 445 ASN cc_start: 0.6981 (m110) cc_final: 0.6295 (t0) REVERT: C 524 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7179 (ptm-80) REVERT: D 7 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8659 (m-70) REVERT: D 50 GLU cc_start: 0.8373 (tp30) cc_final: 0.7983 (tp30) REVERT: D 233 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8526 (mtp85) REVERT: D 354 ASP cc_start: 0.8132 (m-30) cc_final: 0.7792 (p0) REVERT: E 124 ILE cc_start: 0.8350 (tt) cc_final: 0.8047 (mt) REVERT: E 316 GLN cc_start: 0.8059 (mt0) cc_final: 0.7691 (mt0) REVERT: E 324 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7873 (mtm180) REVERT: E 361 ASP cc_start: 0.7612 (m-30) cc_final: 0.7361 (m-30) REVERT: E 363 MET cc_start: 0.8503 (mmt) cc_final: 0.7941 (mmt) REVERT: F 64 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7981 (ptp-110) REVERT: F 74 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7612 (mtp85) REVERT: F 93 SER cc_start: 0.8147 (p) cc_final: 0.7805 (t) REVERT: F 97 LYS cc_start: 0.7280 (mptt) cc_final: 0.6653 (ttpt) REVERT: F 208 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: F 278 MET cc_start: 0.9147 (mmm) cc_final: 0.8469 (mmt) REVERT: G 43 TRP cc_start: 0.9406 (OUTLIER) cc_final: 0.8944 (t-100) REVERT: G 141 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5710 (mm-30) REVERT: G 154 ASP cc_start: 0.8462 (t0) cc_final: 0.8173 (t0) REVERT: G 173 MET cc_start: 0.9063 (ttt) cc_final: 0.8622 (ttt) REVERT: G 225 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8592 (mp10) REVERT: H 7 HIS cc_start: 0.9295 (OUTLIER) cc_final: 0.9058 (m90) REVERT: H 188 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8711 (t80) REVERT: H 208 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: H 253 ARG cc_start: 0.8576 (ttt-90) cc_final: 0.6454 (mmt-90) REVERT: H 326 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7181 (ptm160) REVERT: H 327 GLU cc_start: 0.7857 (tt0) cc_final: 0.7584 (tt0) REVERT: H 363 MET cc_start: 0.9146 (mmt) cc_final: 0.8241 (mmt) REVERT: I 188 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7691 (t80) REVERT: I 193 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8735 (p) REVERT: I 250 GLN cc_start: 0.8259 (mm110) cc_final: 0.7906 (tp-100) REVERT: I 289 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7012 (ptm160) REVERT: I 316 GLN cc_start: 0.8321 (tp40) cc_final: 0.8078 (tp-100) REVERT: L 8 GLN cc_start: 0.7740 (mt0) cc_final: 0.7415 (mt0) REVERT: L 88 MET cc_start: 0.8894 (mtp) cc_final: 0.8634 (ttm) REVERT: N 69 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8185 (ttm-80) REVERT: N 71 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8783 (t) REVERT: N 110 ASP cc_start: 0.7778 (t70) cc_final: 0.7465 (t70) REVERT: N 160 ARG cc_start: 0.8293 (mtp180) cc_final: 0.8088 (mtp180) REVERT: N 206 SER cc_start: 0.8519 (t) cc_final: 0.8201 (p) outliers start: 107 outliers final: 69 residues processed: 429 average time/residue: 0.2100 time to fit residues: 139.8358 Evaluate side-chains 420 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 331 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 188 PHE Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 326 ARG Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain L residue 153 ASN Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 202 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 309 optimal weight: 40.0000 chunk 274 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN H 18 ASN J 23 ASN L 153 ASN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120563 restraints weight = 40178.685| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.92 r_work: 0.3190 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29812 Z= 0.151 Angle : 0.667 11.575 41120 Z= 0.328 Chirality : 0.051 0.629 4655 Planarity : 0.005 0.058 4869 Dihedral : 16.929 159.128 5315 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 4.13 % Allowed : 17.97 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3269 helix: 1.37 (0.14), residues: 1381 sheet: -0.99 (0.21), residues: 477 loop : -0.61 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.023 0.001 TYR N 137 PHE 0.022 0.001 PHE G 226 TRP 0.017 0.001 TRP C 390 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (29812) covalent geometry : angle 0.66662 / 0.33 (41120) hydrogen bonds : bond 0.04085 / 2.86 ( 1357) hydrogen bonds : angle 4.61068 / 3.20 ( 3858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 336 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.2148 (mtt) cc_final: 0.1600 (mtm) REVERT: C 21 ASP cc_start: 0.7995 (t0) cc_final: 0.7615 (t0) REVERT: C 22 VAL cc_start: 0.8391 (t) cc_final: 0.8130 (p) REVERT: C 24 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7628 (pt) REVERT: C 76 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7069 (t) REVERT: C 200 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.4427 (pmt-80) REVERT: C 215 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8551 (pp) REVERT: C 320 GLU cc_start: 0.6807 (mp0) cc_final: 0.6455 (mp0) REVERT: C 357 ASN cc_start: 0.7681 (m-40) cc_final: 0.7342 (m-40) REVERT: C 363 GLN cc_start: 0.6300 (tm-30) cc_final: 0.6053 (tm-30) REVERT: C 438 LYS cc_start: 0.9043 (tttp) cc_final: 0.8656 (ttmt) REVERT: C 445 ASN cc_start: 0.7020 (m110) cc_final: 0.6320 (t0) REVERT: C 524 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7196 (ptm-80) REVERT: D 7 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8642 (m-70) REVERT: D 50 GLU cc_start: 0.8407 (tp30) cc_final: 0.8025 (tp30) REVERT: D 233 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8555 (mtp85) REVERT: E 124 ILE cc_start: 0.8280 (tt) cc_final: 0.8014 (mt) REVERT: E 316 GLN cc_start: 0.8210 (mt0) cc_final: 0.7857 (mt0) REVERT: E 324 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7957 (mtm180) REVERT: E 361 ASP cc_start: 0.7536 (m-30) cc_final: 0.7276 (m-30) REVERT: F 64 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8454 (ptp-170) REVERT: F 97 LYS cc_start: 0.7382 (mptt) cc_final: 0.6763 (ttpt) REVERT: F 208 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: F 278 MET cc_start: 0.9216 (mmm) cc_final: 0.8560 (mmt) REVERT: G 43 TRP cc_start: 0.9426 (OUTLIER) cc_final: 0.8945 (t-100) REVERT: G 141 GLU cc_start: 0.5937 (mm-30) cc_final: 0.5455 (mm-30) REVERT: G 154 ASP cc_start: 0.8389 (t0) cc_final: 0.8097 (t0) REVERT: G 173 MET cc_start: 0.9057 (ttt) cc_final: 0.8583 (ttt) REVERT: H 7 HIS cc_start: 0.9290 (OUTLIER) cc_final: 0.9056 (m90) REVERT: H 188 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8751 (t80) REVERT: H 208 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: H 253 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.6507 (mmt-90) REVERT: H 326 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7271 (ptm160) REVERT: H 363 MET cc_start: 0.9171 (mmt) cc_final: 0.8243 (mmt) REVERT: I 188 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7733 (t80) REVERT: I 193 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8667 (p) REVERT: I 250 GLN cc_start: 0.8388 (mm110) cc_final: 0.7984 (tp-100) REVERT: I 289 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.7284 (ptm160) REVERT: I 316 GLN cc_start: 0.8363 (tp40) cc_final: 0.8124 (tp-100) REVERT: L 8 GLN cc_start: 0.7778 (mt0) cc_final: 0.7454 (mt0) REVERT: L 88 MET cc_start: 0.8902 (mtp) cc_final: 0.8668 (ttm) REVERT: N 71 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8747 (t) REVERT: N 110 ASP cc_start: 0.7744 (t70) cc_final: 0.7395 (t70) REVERT: N 160 ARG cc_start: 0.8274 (mtp180) cc_final: 0.8059 (mtp180) REVERT: N 206 SER cc_start: 0.8527 (t) cc_final: 0.8190 (p) outliers start: 110 outliers final: 71 residues processed: 417 average time/residue: 0.2100 time to fit residues: 137.6359 Evaluate side-chains 411 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 322 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 188 PHE Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 326 ARG Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 32 optimal weight: 7.9990 chunk 276 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 218 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 89 GLN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS H 285 HIS J 23 ASN ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN L 227 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112941 restraints weight = 40111.885| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.86 r_work: 0.3121 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 29812 Z= 0.271 Angle : 0.781 12.204 41120 Z= 0.389 Chirality : 0.057 0.718 4655 Planarity : 0.006 0.075 4869 Dihedral : 17.000 160.139 5315 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 4.05 % Allowed : 18.27 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3269 helix: 1.14 (0.14), residues: 1379 sheet: -1.04 (0.22), residues: 456 loop : -0.78 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 19 TYR 0.022 0.002 TYR F 30 PHE 0.024 0.002 PHE G 226 TRP 0.020 0.002 TRP C 390 HIS 0.008 0.002 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (29812) covalent geometry : angle 0.78139 / 0.39 (41120) hydrogen bonds : bond 0.04707 / 3.25 ( 1357) hydrogen bonds : angle 4.89201 / 3.38 ( 3858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 324 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: C 21 ASP cc_start: 0.8089 (t0) cc_final: 0.7689 (t0) REVERT: C 22 VAL cc_start: 0.8356 (t) cc_final: 0.8108 (p) REVERT: C 24 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7832 (pt) REVERT: C 42 LEU cc_start: 0.8292 (pp) cc_final: 0.8035 (pp) REVERT: C 76 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7522 (t) REVERT: C 200 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.4858 (pmt-80) REVERT: C 215 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8469 (pp) REVERT: C 293 ASP cc_start: 0.8167 (m-30) cc_final: 0.7733 (t0) REVERT: C 357 ASN cc_start: 0.7907 (m-40) cc_final: 0.7487 (m-40) REVERT: C 438 LYS cc_start: 0.9094 (tttp) cc_final: 0.8694 (ttmt) REVERT: C 445 ASN cc_start: 0.7367 (m110) cc_final: 0.6536 (t0) REVERT: D 7 HIS cc_start: 0.9122 (OUTLIER) cc_final: 0.8882 (m-70) REVERT: D 50 GLU cc_start: 0.8518 (tp30) cc_final: 0.8187 (tp30) REVERT: D 233 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8865 (mtp85) REVERT: D 317 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7592 (mm-30) REVERT: F 64 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8006 (ptp-110) REVERT: F 97 LYS cc_start: 0.7708 (mptt) cc_final: 0.6884 (ttpt) REVERT: F 208 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: F 278 MET cc_start: 0.9203 (mmm) cc_final: 0.8581 (mmt) REVERT: F 344 THR cc_start: 0.8497 (m) cc_final: 0.8086 (p) REVERT: G 43 TRP cc_start: 0.9460 (OUTLIER) cc_final: 0.9123 (t-100) REVERT: G 154 ASP cc_start: 0.8297 (t0) cc_final: 0.8038 (t0) REVERT: G 173 MET cc_start: 0.9061 (ttt) cc_final: 0.8579 (ttt) REVERT: H 7 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8848 (m-70) REVERT: H 174 LEU cc_start: 0.8461 (tp) cc_final: 0.8062 (tp) REVERT: H 208 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: H 253 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.6574 (mmt-90) REVERT: H 326 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7605 (ptm160) REVERT: I 193 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8747 (p) REVERT: I 250 GLN cc_start: 0.8400 (mm110) cc_final: 0.7992 (tp-100) REVERT: I 289 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8135 (ptm160) REVERT: I 319 ASN cc_start: 0.8951 (t0) cc_final: 0.8588 (t0) REVERT: I 342 ASN cc_start: 0.5920 (t0) cc_final: 0.5140 (m-40) REVERT: L 8 GLN cc_start: 0.7850 (mt0) cc_final: 0.7591 (mt0) REVERT: L 88 MET cc_start: 0.8926 (mtp) cc_final: 0.8725 (ttm) REVERT: N 71 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8816 (t) REVERT: N 97 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7667 (tptm) REVERT: N 110 ASP cc_start: 0.7895 (t70) cc_final: 0.7420 (t0) REVERT: N 217 ARG cc_start: 0.8393 (ppt-90) cc_final: 0.8189 (ppt170) outliers start: 108 outliers final: 72 residues processed: 402 average time/residue: 0.2079 time to fit residues: 129.6991 Evaluate side-chains 392 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 305 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 326 ARG Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 29 optimal weight: 0.0470 chunk 301 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN H 220 HIS J 23 ASN J 175 HIS L 98 GLN L 227 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117500 restraints weight = 39829.643| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.87 r_work: 0.3205 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29812 Z= 0.141 Angle : 0.688 12.270 41120 Z= 0.338 Chirality : 0.051 0.627 4655 Planarity : 0.005 0.059 4869 Dihedral : 16.933 159.443 5315 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 3.23 % Allowed : 19.40 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3269 helix: 1.33 (0.14), residues: 1374 sheet: -0.98 (0.22), residues: 444 loop : -0.67 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 211 TYR 0.024 0.002 TYR N 137 PHE 0.016 0.002 PHE C 20 TRP 0.019 0.001 TRP C 390 HIS 0.007 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (29812) covalent geometry : angle 0.68787 / 0.34 (41120) hydrogen bonds : bond 0.04168 / 2.92 ( 1357) hydrogen bonds : angle 4.70282 / 3.26 ( 3858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 333 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: C 21 ASP cc_start: 0.8067 (t0) cc_final: 0.7497 (t0) REVERT: C 22 VAL cc_start: 0.8261 (t) cc_final: 0.8059 (p) REVERT: C 24 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7747 (pt) REVERT: C 42 LEU cc_start: 0.8166 (pp) cc_final: 0.7897 (pp) REVERT: C 45 ARG cc_start: 0.7054 (ttt-90) cc_final: 0.6350 (ttp80) REVERT: C 76 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7259 (t) REVERT: C 200 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.4508 (pmt-80) REVERT: C 215 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8512 (pp) REVERT: C 293 ASP cc_start: 0.8172 (m-30) cc_final: 0.7752 (t0) REVERT: C 357 ASN cc_start: 0.7763 (m-40) cc_final: 0.7410 (m-40) REVERT: C 438 LYS cc_start: 0.9050 (tttp) cc_final: 0.8668 (ttmt) REVERT: C 445 ASN cc_start: 0.7240 (m110) cc_final: 0.6501 (t0) REVERT: D 7 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8671 (m-70) REVERT: D 50 GLU cc_start: 0.8488 (tp30) cc_final: 0.8153 (tp30) REVERT: D 233 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8703 (mtp85) REVERT: E 124 ILE cc_start: 0.8291 (tt) cc_final: 0.7943 (mt) REVERT: E 188 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: F 64 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8028 (ptp-110) REVERT: F 208 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: F 278 MET cc_start: 0.9168 (mmm) cc_final: 0.8502 (mmt) REVERT: F 344 THR cc_start: 0.8547 (m) cc_final: 0.8140 (p) REVERT: G 43 TRP cc_start: 0.9439 (OUTLIER) cc_final: 0.9155 (t-100) REVERT: G 141 GLU cc_start: 0.6336 (mm-30) cc_final: 0.5881 (mm-30) REVERT: G 154 ASP cc_start: 0.8309 (t0) cc_final: 0.8060 (t0) REVERT: G 173 MET cc_start: 0.9046 (ttt) cc_final: 0.8519 (ttt) REVERT: G 341 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: H 7 HIS cc_start: 0.9292 (OUTLIER) cc_final: 0.8866 (m90) REVERT: H 208 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: H 241 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8335 (tpt-90) REVERT: H 253 ARG cc_start: 0.8670 (ttt-90) cc_final: 0.6527 (mmt-90) REVERT: H 326 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7443 (ptm160) REVERT: I 193 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8716 (p) REVERT: I 250 GLN cc_start: 0.8348 (mm110) cc_final: 0.7862 (tp-100) REVERT: I 289 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.7247 (ptm160) REVERT: I 316 GLN cc_start: 0.8457 (tp40) cc_final: 0.8251 (tp-100) REVERT: I 342 ASN cc_start: 0.5750 (t0) cc_final: 0.5033 (m-40) REVERT: J 44 MET cc_start: 0.8825 (mmt) cc_final: 0.8599 (mmt) REVERT: L 8 GLN cc_start: 0.7777 (mt0) cc_final: 0.7521 (mt0) REVERT: L 88 MET cc_start: 0.8897 (mtp) cc_final: 0.8669 (ttm) REVERT: N 110 ASP cc_start: 0.7836 (t70) cc_final: 0.7337 (t0) outliers start: 86 outliers final: 59 residues processed: 398 average time/residue: 0.2143 time to fit residues: 132.2504 Evaluate side-chains 391 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 326 ARG Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 336 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS J 23 ASN J 167 GLN J 175 HIS L 98 GLN L 227 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117730 restraints weight = 40318.778| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.87 r_work: 0.3128 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 29812 Z= 0.206 Angle : 0.785 59.199 41120 Z= 0.417 Chirality : 0.053 0.970 4655 Planarity : 0.005 0.061 4869 Dihedral : 16.925 159.447 5313 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Rotamer: Outliers : 3.26 % Allowed : 19.62 % Favored : 77.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3269 helix: 1.31 (0.14), residues: 1374 sheet: -0.98 (0.22), residues: 439 loop : -0.67 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 72 TYR 0.021 0.002 TYR N 137 PHE 0.015 0.002 PHE C 20 TRP 0.018 0.001 TRP C 390 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (29812) covalent geometry : angle 0.78500 / 0.42 (41120) hydrogen bonds : bond 0.04194 / 2.93 ( 1357) hydrogen bonds : angle 4.69936 / 3.26 ( 3858) =============================================================================== Job complete usr+sys time: 8436.58 seconds wall clock time: 144 minutes 50.81 seconds (8690.81 seconds total)