Starting phenix.real_space_refine on Mon Sep 14 05:03:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igx_52861/09_2026/9igx_52861.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igx_52861/09_2026/9igx_52861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9igx_52861/09_2026/9igx_52861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igx_52861/09_2026/9igx_52861.map" model { file = "/net/cci-nas-00/data/ceres_data/9igx_52861/09_2026/9igx_52861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igx_52861/09_2026/9igx_52861.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 297 5.49 5 S 76 5.16 5 C 16619 2.51 5 N 4899 2.21 5 O 5828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 27719 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3768 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 27, 'TRANS': 472} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 7, 'GLU:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 12, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 184 Chain: "L" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3947 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 26, 'TRANS': 497} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 7, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 5, 'ASP:plan': 3, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 762 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 778 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 636 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 676 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3804 Classifications: {'peptide': 490} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 6 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 2, 'PHE:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "N" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4028 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 490} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3037 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3069 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Time building chain proxies: 6.37, per 1000 atoms: 0.23 Number of scatterers: 27719 At special positions: 0 Unit cell: (109.592, 145.024, 228.248, 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 76 16.00 P 297 15.00 O 5828 8.00 N 4899 7.00 C 16619 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: 2.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5316 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 26 sheets defined 46.2% alpha, 9.5% beta 85 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'K' and resid 58 through 77 Processing helix chain 'K' and resid 112 through 122 removed outlier: 3.782A pdb=" N PHE K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 135 removed outlier: 3.997A pdb=" N GLY K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 155 Processing helix chain 'K' and resid 179 through 196 removed outlier: 3.979A pdb=" N ALA K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 219 removed outlier: 3.704A pdb=" N ARG K 218 " --> pdb=" O LEU K 215 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP K 219 " --> pdb=" O PHE K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 251 removed outlier: 3.670A pdb=" N ALA K 248 " --> pdb=" O ARG K 244 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS K 249 " --> pdb=" O LYS K 245 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU K 250 " --> pdb=" O VAL K 246 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR K 251 " --> pdb=" O ARG K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 339 Processing helix chain 'K' and resid 375 through 393 removed outlier: 4.326A pdb=" N SER K 379 " --> pdb=" O VAL K 375 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR K 380 " --> pdb=" O ILE K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 455 through 468 Processing helix chain 'K' and resid 480 through 495 Processing helix chain 'K' and resid 510 through 519 Processing helix chain 'K' and resid 520 through 530 Processing helix chain 'L' and resid 17 through 22 removed outlier: 3.739A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 49 Processing helix chain 'L' and resid 87 through 96 Processing helix chain 'L' and resid 106 through 123 removed outlier: 3.566A pdb=" N GLU L 121 " --> pdb=" O VAL L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 158 Processing helix chain 'L' and resid 198 through 223 removed outlier: 8.547A pdb=" N GLU L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP L 219 " --> pdb=" O LEU L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'L' and resid 235 through 239 Processing helix chain 'L' and resid 304 through 308 Processing helix chain 'L' and resid 324 through 331 Processing helix chain 'L' and resid 352 through 356 Processing helix chain 'L' and resid 372 through 388 Processing helix chain 'L' and resid 447 through 462 Processing helix chain 'L' and resid 484 through 500 removed outlier: 4.012A pdb=" N GLN L 488 " --> pdb=" O ASN L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 517 removed outlier: 3.704A pdb=" N TRP L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 536 Proline residue: L 529 - end of helix Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.368A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.506A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.579A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.589A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.554A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.579A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.592A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.535A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.581A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.833A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.509A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.521A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.814A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'M' and resid 45 through 50 Processing helix chain 'M' and resid 58 through 78 removed outlier: 3.690A pdb=" N ILE M 64 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 122 removed outlier: 4.001A pdb=" N PHE M 122 " --> pdb=" O GLU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 136 Processing helix chain 'M' and resid 142 through 156 removed outlier: 3.995A pdb=" N VAL M 146 " --> pdb=" O SER M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 197 Processing helix chain 'M' and resid 239 through 250 Processing helix chain 'M' and resid 332 through 337 Processing helix chain 'M' and resid 377 through 393 removed outlier: 3.667A pdb=" N ILE M 387 " --> pdb=" O SER M 383 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS M 388 " --> pdb=" O ALA M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 443 Processing helix chain 'M' and resid 455 through 470 removed outlier: 3.549A pdb=" N VAL M 459 " --> pdb=" O THR M 455 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS M 468 " --> pdb=" O ALA M 464 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU M 469 " --> pdb=" O ILE M 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 495 removed outlier: 3.684A pdb=" N GLN M 484 " --> pdb=" O ASN M 480 " (cutoff:3.500A) Processing helix chain 'M' and resid 511 through 519 Processing helix chain 'M' and resid 520 through 530 removed outlier: 3.696A pdb=" N GLU M 524 " --> pdb=" O SER M 520 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 47 removed outlier: 4.940A pdb=" N ARG N 44 " --> pdb=" O MET N 40 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN N 45 " --> pdb=" O PHE N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 97 Processing helix chain 'N' and resid 111 through 120 Processing helix chain 'N' and resid 146 through 154 removed outlier: 4.148A pdb=" N ILE N 150 " --> pdb=" O GLN N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 197 removed outlier: 4.085A pdb=" N ILE N 197 " --> pdb=" O LEU N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 216 Processing helix chain 'N' and resid 218 through 224 removed outlier: 3.599A pdb=" N LEU N 221 " --> pdb=" O GLU N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 238 removed outlier: 3.960A pdb=" N VAL N 236 " --> pdb=" O LYS N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 331 Processing helix chain 'N' and resid 347 through 351 Processing helix chain 'N' and resid 352 through 356 Processing helix chain 'N' and resid 370 through 387 removed outlier: 4.329A pdb=" N LEU N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 441 removed outlier: 3.528A pdb=" N SER N 441 " --> pdb=" O LEU N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 460 removed outlier: 3.565A pdb=" N SER N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 468 through 470 No H-bonds generated for 'chain 'N' and resid 468 through 470' Processing helix chain 'N' and resid 478 through 482 removed outlier: 3.564A pdb=" N LYS N 481 " --> pdb=" O PRO N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 484 through 499 removed outlier: 3.631A pdb=" N GLN N 488 " --> pdb=" O ASN N 484 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU N 499 " --> pdb=" O LEU N 495 " (cutoff:3.500A) Processing helix chain 'N' and resid 509 through 517 removed outlier: 3.581A pdb=" N TRP N 513 " --> pdb=" O GLN N 509 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN N 517 " --> pdb=" O TRP N 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 527 Processing helix chain 'N' and resid 528 through 537 removed outlier: 4.455A pdb=" N LYS N 532 " --> pdb=" O ILE N 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 102 through 109 removed outlier: 6.629A pdb=" N VAL K 85 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU K 107 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU K 83 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER K 37 " --> pdb=" O ARG K 165 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET K 167 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE K 39 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE K 169 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU K 41 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS K 164 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 261 through 262 removed outlier: 5.627A pdb=" N GLY K 349 " --> pdb=" O LEU K 397 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU K 397 " --> pdb=" O GLY K 349 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N VAL K 394 " --> pdb=" O PRO K 415 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE K 367 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 286 through 288 Processing sheet with id=AA4, first strand: chain 'L' and resid 13 through 14 removed outlier: 7.227A pdb=" N CYS L 13 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE L 134 " --> pdb=" O PHE L 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 59 removed outlier: 4.207A pdb=" N LEU L 56 " --> pdb=" O HIS L 82 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS L 82 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU L 58 " --> pdb=" O HIS L 80 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N HIS L 80 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 247 through 251 Processing sheet with id=AA7, first strand: chain 'L' and resid 339 through 347 removed outlier: 5.601A pdb=" N PHE L 340 " --> pdb=" O ALA L 396 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA L 396 " --> pdb=" O PHE L 340 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL L 342 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG L 394 " --> pdb=" O VAL L 342 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N MET L 389 " --> pdb=" O PRO L 410 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLN L 423 " --> pdb=" O GLN L 360 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLN L 360 " --> pdb=" O GLN L 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 464 through 467 Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.728A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.618A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.482A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'G' and resid 100 through 102 removed outlier: 3.941A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.834A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'M' and resid 36 through 40 removed outlier: 3.777A pdb=" N ASP M 109 " --> pdb=" O LEU M 83 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL M 85 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU M 107 " --> pdb=" O VAL M 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 255 through 257 removed outlier: 6.880A pdb=" N ILE M 273 " --> pdb=" O LEU M 256 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE M 367 " --> pdb=" O TYR M 274 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE M 432 " --> pdb=" O VAL M 368 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA M 396 " --> pdb=" O LEU M 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL M 394 " --> pdb=" O PRO M 415 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY M 349 " --> pdb=" O LEU M 397 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 260 through 261 Processing sheet with id=AC2, first strand: chain 'M' and resid 286 through 288 removed outlier: 3.646A pdb=" N LEU M 288 " --> pdb=" O ILE N 311 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE N 311 " --> pdb=" O LEU M 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 325 through 329 removed outlier: 3.614A pdb=" N TYR M 322 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 375 through 376 Processing sheet with id=AC5, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.816A pdb=" N CYS N 13 " --> pdb=" O PHE N 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'N' and resid 57 through 59 removed outlier: 3.545A pdb=" N THR N 78 " --> pdb=" O LEU N 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 247 through 253 removed outlier: 3.834A pdb=" N LEU N 257 " --> pdb=" O ILE N 253 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS N 265 " --> pdb=" O LYS N 363 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS N 363 " --> pdb=" O LYS N 265 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N GLN N 360 " --> pdb=" O GLN N 423 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN N 423 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 464 through 467 removed outlier: 3.868A pdb=" N THR N 472 " --> pdb=" O ASP N 467 " (cutoff:3.500A) 1001 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 360 hydrogen bond angles 0 basepair planarities 85 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7650 1.34 - 1.46: 6762 1.46 - 1.58: 13697 1.58 - 1.70: 593 1.70 - 1.82: 123 Bond restraints: 28825 Sorted by residual: bond pdb=" C3' DG J 128 " pdb=" C2' DG J 128 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DC J 132 " pdb=" C2' DC J 132 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA J 39 " pdb=" C2' DA J 39 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DA J 119 " pdb=" C2' DA J 119 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC J 147 " pdb=" C2' DC J 147 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 28820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 39789 2.46 - 4.92: 455 4.92 - 7.39: 25 7.39 - 9.85: 2 9.85 - 12.31: 3 Bond angle restraints: 40274 Sorted by residual: angle pdb=" O4' DG J 28 " pdb=" C4' DG J 28 " pdb=" C3' DG J 28 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.22e+01 angle pdb=" O4' DG I 135 " pdb=" C4' DG I 135 " pdb=" C3' DG I 135 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.19e+01 angle pdb=" O4' DA I 55 " pdb=" C4' DA I 55 " pdb=" C3' DA I 55 " ideal model delta sigma weight residual 106.00 102.72 3.28 6.00e-01 2.78e+00 3.00e+01 angle pdb=" O4' DA J 74 " pdb=" C4' DA J 74 " pdb=" C3' DA J 74 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.70e+01 angle pdb=" O4' DC J 78 " pdb=" C4' DC J 78 " pdb=" C3' DC J 78 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 ... (remaining 40269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 14888 35.39 - 70.78: 1812 70.78 - 106.16: 85 106.16 - 141.55: 5 141.55 - 176.94: 6 Dihedral angle restraints: 16796 sinusoidal: 8628 harmonic: 8168 Sorted by residual: dihedral pdb=" CA GLY G 22 " pdb=" C GLY G 22 " pdb=" N LEU G 23 " pdb=" CA LEU G 23 " ideal model delta harmonic sigma weight residual -180.00 -153.00 -27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA HIS K 137 " pdb=" C HIS K 137 " pdb=" N GLY K 138 " pdb=" CA GLY K 138 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C4' DG I 131 " pdb=" C3' DG I 131 " pdb=" O3' DG I 131 " pdb=" P DT I 132 " ideal model delta sinusoidal sigma weight residual 220.00 43.06 176.94 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 16793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3236 0.039 - 0.078: 980 0.078 - 0.117: 354 0.117 - 0.156: 56 0.156 - 0.195: 6 Chirality restraints: 4632 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 -2.40 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU D 77 " pdb=" CB LEU D 77 " pdb=" CD1 LEU D 77 " pdb=" CD2 LEU D 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 4629 not shown) Planarity restraints: 4136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO G 80 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 97 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C LEU B 97 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 97 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 98 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 106 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C HIS H 106 " -0.040 2.00e-02 2.50e+03 pdb=" O HIS H 106 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA H 107 " 0.013 2.00e-02 2.50e+03 ... (remaining 4133 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2840 2.74 - 3.28: 29256 3.28 - 3.82: 52835 3.82 - 4.36: 58591 4.36 - 4.90: 91355 Nonbonded interactions: 234877 Sorted by model distance: nonbonded pdb=" O LYS H 113 " pdb=" OG1 THR H 116 " model vdw 2.203 3.040 nonbonded pdb=" OD2 ASP H 65 " pdb=" OH TYR B 98 " model vdw 2.207 3.040 nonbonded pdb=" O2 DC I 133 " pdb=" N2 DG J 21 " model vdw 2.215 3.120 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 125 " model vdw 2.233 3.040 ... (remaining 234872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 102 or (resid 103 through 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 132 or (resid 133 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 39 and (name N or name CA or name C or name O or name CB \ )) or resid 40 through 133)) } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB )) or resid 85 through 100)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 12 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 118)) selection = (chain 'G' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 26 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 122)) } ncs_group { reference = (chain 'K' and (resid 34 through 78 or (resid 79 through 80 and (name N or name \ CA or name C or name O or name CB )) or resid 81 through 86 or resid 89 through \ 91 or (resid 92 through 94 and (name N or name CA or name C or name O or name CB \ )) or resid 95 through 105 or (resid 106 and (name N or name CA or name C or na \ me O or name CB )) or resid 107 through 122 or (resid 123 and (name N or name CA \ or name C or name O or name CB )) or resid 124 through 138 or resid 140 through \ 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or r \ esid 155 through 168 or (resid 169 and (name N or name CA or name C or name O or \ name CB )) or resid 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 173 through 193 or (resid 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 202 or (resid 203 and (name \ N or name CA or name C or name O or name CB )) or resid 204 through 210 or (res \ id 211 and (name N or name CA or name C or name O or name CB )) or resid 212 thr \ ough 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) \ or resid 219 through 225 or resid 231 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB )) or resid 245 through 248 or (resid 249 \ and (name N or name CA or name C or name O or name CB )) or resid 250 through 25 \ 8 or (resid 259 and (name N or name CA or name C or name O or name CB )) or resi \ d 260 through 289 or (resid 290 through 291 and (name N or name CA or name C or \ name O or name CB )) or resid 292 through 333 or (resid 334 and (name N or name \ CA or name C or name O or name CB )) or resid 335 through 360 or resid 362 throu \ gh 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or \ resid 398 through 423 or (resid 424 and (name N or name CA or name C or name O \ or name CB )) or resid 425 through 438 or (resid 439 through 440 and (name N or \ name CA or name C or name O or name CB )) or resid 441 through 443 or (resid 444 \ and (name N or name CA or name C or name O or name CB )) or resid 446 through 5 \ 01 or resid 503 through 533)) selection = (chain 'M' and (resid 34 through 45 or (resid 46 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 59 or (resid 60 and (na \ me N or name CA or name C or name O or name CB )) or resid 61 through 73 or (res \ id 74 and (name N or name CA or name C or name O or name CB )) or resid 75 throu \ gh 116 or (resid 117 through 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 or (resid 128 and (name N \ or name CA or name C or name O or name CB )) or resid 129 or (resid 130 and (na \ me N or name CA or name C or name O or name CB )) or resid 131 through 132 or (r \ esid 133 and (name N or name CA or name C or name O or name CB )) or resid 134 t \ hrough 136 or (resid 137 and (name N or name CA or name C or name O or name CB ) \ ) or resid 138 through 164 or (resid 165 and (name N or name CA or name C or nam \ e O or name CB )) or resid 166 or (resid 167 and (name N or name CA or name C or \ name O or name CB )) or resid 168 through 177 or (resid 178 and (name N or name \ CA or name C or name O or name CB )) or resid 179 through 186 or (resid 187 and \ (name N or name CA or name C or name O or name CB )) or resid 188 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 253 or (resid 254 through 255 and (name N or name CA or name C or nam \ e O or name CB )) or resid 256 through 261 or (resid 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 290 or (r \ esid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 t \ hrough 296 or (resid 297 and (name N or name CA or name C or name O or name CB ) \ ) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB )) or resid 312 through 317 or (resid 318 and (name N or name \ CA or name C or name O or name CB )) or resid 319 through 321 or (resid 322 and \ (name N or name CA or name C or name O or name CB )) or resid 323 through 339 o \ r (resid 340 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 41 through 344 or (resid 345 and (name N or name CA or name C or name O or name \ CB )) or resid 346 through 362 or (resid 363 and (name N or name CA or name C or \ name O or name CB )) or resid 364 through 392 or (resid 393 and (name N or name \ CA or name C or name O or name CB )) or resid 394 through 398 or (resid 399 thr \ ough 400 and (name N or name CA or name C or name O or name CB )) or resid 401 t \ hrough 408 or (resid 409 and (name N or name CA or name C or name O or name CB ) \ ) or resid 410 through 435 or (resid 436 and (name N or name CA or name C or nam \ e O or name CB )) or resid 437 through 441 or (resid 442 and (name N or name CA \ or name C or name O or name CB )) or resid 443 through 457 or (resid 458 and (na \ me N or name CA or name C or name O or name CB )) or resid 459 through 469 or (r \ esid 470 through 471 and (name N or name CA or name C or name O or name CB )) or \ resid 472 through 473 or (resid 474 and (name N or name CA or name C or name O \ or name CB )) or resid 475 through 477 or (resid 478 and (name N or name CA or n \ ame C or name O or name CB )) or resid 479 or (resid 480 and (name N or name CA \ or name C or name O or name CB )) or resid 481 through 482 or (resid 483 and (na \ me N or name CA or name C or name O or name CB )) or resid 484 through 486 or (r \ esid 487 and (name N or name CA or name C or name O or name CB )) or resid 488 t \ hrough 501 or resid 503 through 513 or (resid 514 and (name N or name CA or name \ C or name O or name CB )) or resid 515 or (resid 516 and (name N or name CA or \ name C or name O or name CB )) or resid 517 through 533)) } ncs_group { reference = (chain 'L' and (resid 12 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 21 or (resid 22 and (name N or nam \ e CA or name C or name O or name CB )) or resid 23 through 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 through 71 or (r \ esid 72 through 73 and (name N or name CA or name C or name O or name CB )) or r \ esid 74 through 81 or (resid 82 through 84 and (name N or name CA or name C or n \ ame O or name CB )) or resid 85 through 119 or (resid 120 and (name N or name CA \ or name C or name O or name CB )) or resid 121 through 158 or resid 181 through \ 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 through 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 through 289 or (resid 290 and (name N or name CA or nam \ e C or name O or name CB )) or resid 291 through 299 or (resid 300 and (name N o \ r name CA or name C or name O or name CB )) or resid 301 through 314 or (resid 3 \ 15 through 316 and (name N or name CA or name C or name O or name CB )) or resid \ 317 through 338 or (resid 339 through 340 and (name N or name CA or name C or n \ ame O or name CB )) or resid 341 through 403 or (resid 404 through 405 and (name \ N or name CA or name C or name O or name CB )) or resid 406 through 442 or (res \ id 443 and (name N or name CA or name C or name O or name CB )) or resid 444 thr \ ough 451 or (resid 452 through 453 and (name N or name CA or name C or name O or \ name CB )) or resid 454 through 543)) selection = (chain 'N' and (resid 12 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 43 or (r \ esid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thr \ ough 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or \ resid 74 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 82 or (resid 83 through 84 and (name N or name CA \ or name C or name O or name CB )) or resid 85 through 88 or (resid 89 and (name \ N or name CA or name C or name O or name CB )) or resid 90 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB )) or resid 93 through \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 113 or (resid 114 and (name N or name CA or name C or name O or na \ me CB )) or resid 115 through 118 or (resid 119 through 120 and (name N or name \ CA or name C or name O or name CB )) or resid 121 or (resid 122 and (name N or n \ ame CA or name C or name O or name CB )) or resid 123 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 12 \ 9 or (resid 130 and (name N or name CA or name C or name O or name CB )) or resi \ d 131 through 136 or (resid 137 through 138 and (name N or name CA or name C or \ name O or name CB )) or resid 139 through 140 or (resid 141 and (name N or name \ CA or name C or name O or name CB )) or resid 142 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 154 or \ (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 6 through 208 or (resid 209 through 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 232 or (resid 233 and (name N or name CA o \ r name C or name O or name CB )) or resid 234 through 275 or (resid 276 and (nam \ e N or name CA or name C or name O or name CB )) or resid 277 through 281 or (re \ sid 282 and (name N or name CA or name C or name O or name CB )) or resid 283 th \ rough 285 or (resid 286 through 287 and (name N or name CA or name C or name O o \ r name CB )) or resid 288 through 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB )) or resid 296 through 305 or (resid 306 and (name N \ or name CA or name C or name O or name CB )) or resid 307 through 310 or (resid \ 311 through 312 and (name N or name CA or name C or name O or name CB )) or resi \ d 313 through 322 or (resid 323 and (name N or name CA or name C or name O or na \ me CB )) or resid 324 or (resid 325 and (name N or name CA or name C or name O o \ r name CB )) or resid 326 through 329 or (resid 330 through 332 and (name N or n \ ame CA or name C or name O or name CB )) or resid 333 or (resid 334 and (name N \ or name CA or name C or name O or name CB )) or resid 335 through 337 or (resid \ 338 through 340 and (name N or name CA or name C or name O or name CB )) or resi \ d 341 through 370 or (resid 371 through 374 and (name N or name CA or name C or \ name O or name CB )) or resid 375 through 404 or (resid 405 and (name N or name \ CA or name C or name O or name CB )) or resid 406 through 418 or (resid 419 and \ (name N or name CA or name C or name O or name CB )) or resid 420 through 423 or \ (resid 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 or (resid 426 through 427 and (name N or name CA or name C or name O or name C \ B )) or resid 428 through 429 or (resid 430 and (name N or name CA or name C or \ name O or name CB )) or resid 431 through 470 or (resid 471 and (name N or name \ CA or name C or name O or name CB )) or resid 472 through 485 or (resid 486 and \ (name N or name CA or name C or name O or name CB )) or resid 487 through 491 or \ (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 3 or (resid 494 and (name N or name CA or name C or name O or name CB )) or resi \ d 495 through 496 or (resid 497 through 498 and (name N or name CA or name C or \ name O or name CB )) or resid 499 through 501 or (resid 502 and (name N or name \ CA or name C or name O or name CB )) or resid 503 through 514 or (resid 515 and \ (name N or name CA or name C or name O or name CB )) or resid 516 through 533 or \ (resid 534 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 5 through 543)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.410 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.290 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28825 Z= 0.357 Angle : 0.667 12.308 40274 Z= 0.515 Chirality : 0.043 0.195 4632 Planarity : 0.004 0.063 4136 Dihedral : 24.851 176.938 11480 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 0.52 % Allowed : 33.97 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2757 helix: 1.23 (0.16), residues: 1186 sheet: -1.67 (0.33), residues: 256 loop : -1.84 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 32 TYR 0.011 0.001 TYR D 37 PHE 0.017 0.001 PHE L 59 TRP 0.003 0.001 TRP L 513 HIS 0.007 0.001 HIS N 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.36 (28825) covalent geometry : angle 0.66664 / 0.51 (40274) hydrogen bonds : bond 0.19150 / 13.18 ( 1197) hydrogen bonds : angle 7.89876 / 5.60 ( 3225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8290 (mmm) cc_final: 0.7918 (mmt) REVERT: N 210 MET cc_start: 0.5751 (mmm) cc_final: 0.5532 (ptt) outliers start: 12 outliers final: 3 residues processed: 112 average time/residue: 0.1622 time to fit residues: 31.7273 Evaluate side-chains 101 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain N residue 23 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 106 GLN L 509 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN M 480 ASN N 152 HIS N 402 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.098279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.056679 restraints weight = 148829.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056299 restraints weight = 58828.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.056501 restraints weight = 33847.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.057001 restraints weight = 26485.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.057069 restraints weight = 23185.744| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28825 Z= 0.237 Angle : 0.698 8.067 40274 Z= 0.389 Chirality : 0.048 0.346 4632 Planarity : 0.005 0.069 4136 Dihedral : 26.841 177.197 6251 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 3.01 % Allowed : 32.36 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2757 helix: 1.24 (0.15), residues: 1210 sheet: -1.63 (0.34), residues: 248 loop : -1.84 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 254 TYR 0.011 0.001 TYR C 39 PHE 0.016 0.001 PHE N 59 TRP 0.006 0.001 TRP L 513 HIS 0.015 0.001 HIS N 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.24 (28825) covalent geometry : angle 0.69769 / 0.39 (40274) hydrogen bonds : bond 0.08159 / 5.12 ( 1197) hydrogen bonds : angle 5.62595 / 4.00 ( 3225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 99 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: L 115 MET cc_start: 0.4259 (tmm) cc_final: 0.3742 (ptt) REVERT: C 112 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: F 95 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7978 (mtp85) REVERT: G 63 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9299 (mp) REVERT: A 50 GLU cc_start: 0.8348 (mp0) cc_final: 0.8143 (mp0) REVERT: B 84 MET cc_start: 0.8444 (mmm) cc_final: 0.8056 (mmt) REVERT: B 85 ASP cc_start: 0.8506 (m-30) cc_final: 0.8244 (m-30) REVERT: N 210 MET cc_start: 0.5850 (mmm) cc_final: 0.5644 (ptt) outliers start: 69 outliers final: 26 residues processed: 165 average time/residue: 0.1593 time to fit residues: 45.4643 Evaluate side-chains 126 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain M residue 480 ASN Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 25 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 94 optimal weight: 40.0000 chunk 265 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.099139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.057698 restraints weight = 152326.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.057513 restraints weight = 60827.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.057948 restraints weight = 34782.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.058149 restraints weight = 26255.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.058159 restraints weight = 22673.612| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28825 Z= 0.165 Angle : 0.622 8.111 40274 Z= 0.350 Chirality : 0.045 0.343 4632 Planarity : 0.004 0.065 4136 Dihedral : 27.063 174.696 6245 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 3.28 % Allowed : 31.79 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2757 helix: 1.34 (0.15), residues: 1229 sheet: -1.73 (0.34), residues: 250 loop : -1.85 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 301 TYR 0.008 0.001 TYR B 72 PHE 0.017 0.001 PHE M 340 TRP 0.005 0.001 TRP L 513 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (28825) covalent geometry : angle 0.62159 / 0.35 (40274) hydrogen bonds : bond 0.06733 / 4.25 ( 1197) hydrogen bonds : angle 5.15560 / 3.65 ( 3225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 104 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 348 MET cc_start: 0.5159 (pmm) cc_final: 0.4828 (pmm) REVERT: L 115 MET cc_start: 0.4397 (tmm) cc_final: 0.3846 (ptt) REVERT: C 112 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: F 95 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7919 (mtp85) REVERT: G 63 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9256 (mp) REVERT: B 84 MET cc_start: 0.8448 (mmm) cc_final: 0.7891 (mmm) REVERT: B 85 ASP cc_start: 0.8324 (m-30) cc_final: 0.8085 (m-30) REVERT: M 48 MET cc_start: -0.0521 (tpp) cc_final: -0.1137 (tpt) REVERT: N 418 CYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5956 (t) outliers start: 75 outliers final: 37 residues processed: 177 average time/residue: 0.1665 time to fit residues: 50.2502 Evaluate side-chains 137 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 427 VAL Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 146 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 chunk 185 optimal weight: 0.6980 chunk 246 optimal weight: 30.0000 chunk 235 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 overall best weight: 6.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 304 ASN C 38 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.095509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.053160 restraints weight = 150341.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053661 restraints weight = 65442.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.053322 restraints weight = 43331.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053640 restraints weight = 34978.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053625 restraints weight = 27463.950| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 28825 Z= 0.384 Angle : 0.805 9.575 40274 Z= 0.436 Chirality : 0.051 0.440 4632 Planarity : 0.005 0.073 4136 Dihedral : 27.186 174.179 6245 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 5.28 % Allowed : 31.53 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.97 (0.16), residues: 2757 helix: 0.85 (0.15), residues: 1232 sheet: -1.80 (0.34), residues: 244 loop : -1.95 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 134 TYR 0.027 0.002 TYR F 88 PHE 0.019 0.002 PHE K 211 TRP 0.007 0.001 TRP L 513 HIS 0.011 0.002 HIS K 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.38 (28825) covalent geometry : angle 0.80535 / 0.44 (40274) hydrogen bonds : bond 0.08042 / 5.24 ( 1197) hydrogen bonds : angle 5.67823 / 4.03 ( 3225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 92 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.4274 (tmm) cc_final: 0.3659 (ptt) REVERT: C 11 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7443 (mmp80) REVERT: C 112 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: E 109 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9233 (tt) REVERT: F 95 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7924 (mtp85) REVERT: G 63 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9408 (mp) REVERT: B 84 MET cc_start: 0.8745 (mmm) cc_final: 0.8036 (mmm) REVERT: B 85 ASP cc_start: 0.8610 (m-30) cc_final: 0.8314 (m-30) outliers start: 121 outliers final: 77 residues processed: 209 average time/residue: 0.1752 time to fit residues: 60.8927 Evaluate side-chains 171 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 89 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 437 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 435 PHE Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 32 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 260 optimal weight: 40.0000 chunk 249 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 198 optimal weight: 40.0000 chunk 183 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.097809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.056393 restraints weight = 147981.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.055883 restraints weight = 59835.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056054 restraints weight = 34688.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056509 restraints weight = 26910.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.056690 restraints weight = 23692.204| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28825 Z= 0.244 Angle : 0.681 9.843 40274 Z= 0.375 Chirality : 0.047 0.372 4632 Planarity : 0.004 0.069 4136 Dihedral : 27.231 176.642 6245 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 4.28 % Allowed : 32.27 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2757 helix: 1.04 (0.15), residues: 1231 sheet: -1.88 (0.34), residues: 250 loop : -1.93 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 403 TYR 0.012 0.001 TYR G 50 PHE 0.017 0.001 PHE L 59 TRP 0.006 0.001 TRP L 513 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (28825) covalent geometry : angle 0.68120 / 0.37 (40274) hydrogen bonds : bond 0.06816 / 4.38 ( 1197) hydrogen bonds : angle 5.32248 / 3.77 ( 3225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 96 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.4422 (tmm) cc_final: 0.3806 (ptt) REVERT: C 112 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: D 73 GLU cc_start: 0.8943 (tp30) cc_final: 0.8740 (tp30) REVERT: E 94 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8016 (mt-10) REVERT: F 95 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7968 (mtp85) REVERT: G 63 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9400 (mp) REVERT: H 56 MET cc_start: 0.9212 (tpp) cc_final: 0.8839 (tpp) REVERT: A 50 GLU cc_start: 0.8477 (mp0) cc_final: 0.8099 (mp0) REVERT: B 84 MET cc_start: 0.8538 (mmm) cc_final: 0.7925 (mmm) REVERT: B 85 ASP cc_start: 0.8437 (m-30) cc_final: 0.8200 (m-30) REVERT: N 210 MET cc_start: 0.5905 (mmm) cc_final: 0.5701 (ptt) REVERT: N 418 CYS cc_start: 0.6360 (OUTLIER) cc_final: 0.5985 (t) outliers start: 98 outliers final: 69 residues processed: 190 average time/residue: 0.1593 time to fit residues: 52.2889 Evaluate side-chains 166 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 93 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 421 ASP Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain M residue 486 HIS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 150 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 268 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 192 optimal weight: 0.0370 chunk 122 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 overall best weight: 1.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.098785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.057208 restraints weight = 151396.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056693 restraints weight = 60020.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.056860 restraints weight = 34873.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.057337 restraints weight = 27392.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.057644 restraints weight = 23777.060| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28825 Z= 0.149 Angle : 0.620 11.268 40274 Z= 0.341 Chirality : 0.045 0.379 4632 Planarity : 0.004 0.064 4136 Dihedral : 27.186 178.480 6245 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 3.28 % Allowed : 32.97 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2757 helix: 1.34 (0.15), residues: 1231 sheet: -1.84 (0.34), residues: 248 loop : -1.84 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 11 TYR 0.018 0.001 TYR F 88 PHE 0.016 0.001 PHE L 59 TRP 0.004 0.001 TRP L 513 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (28825) covalent geometry : angle 0.62008 / 0.34 (40274) hydrogen bonds : bond 0.05971 / 3.82 ( 1197) hydrogen bonds : angle 4.91532 / 3.47 ( 3225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 103 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.4525 (tmm) cc_final: 0.3855 (ptt) REVERT: C 112 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: D 83 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8600 (ttm-80) REVERT: E 94 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8016 (mt-10) REVERT: F 95 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7979 (mtp85) REVERT: G 63 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9247 (mp) REVERT: A 50 GLU cc_start: 0.8496 (mp0) cc_final: 0.8078 (mp0) REVERT: A 68 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8585 (tp-100) REVERT: B 84 MET cc_start: 0.8436 (mmm) cc_final: 0.7938 (mmm) REVERT: B 97 LEU cc_start: 0.9138 (tp) cc_final: 0.8846 (tt) REVERT: N 302 GLU cc_start: 0.3985 (OUTLIER) cc_final: 0.3430 (tm-30) REVERT: N 418 CYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6038 (t) outliers start: 75 outliers final: 49 residues processed: 176 average time/residue: 0.1642 time to fit residues: 49.1039 Evaluate side-chains 155 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 421 ASP Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 231 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 97 optimal weight: 50.0000 chunk 187 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 275 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 359 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.097278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.055630 restraints weight = 148673.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.055505 restraints weight = 59614.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.055930 restraints weight = 34440.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056361 restraints weight = 25616.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056189 restraints weight = 22820.622| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28825 Z= 0.264 Angle : 0.690 11.145 40274 Z= 0.376 Chirality : 0.046 0.373 4632 Planarity : 0.004 0.074 4136 Dihedral : 27.234 174.411 6245 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 4.28 % Allowed : 32.27 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.72 (0.16), residues: 2757 helix: 1.14 (0.15), residues: 1235 sheet: -1.87 (0.34), residues: 248 loop : -1.87 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.056 0.002 TYR F 88 PHE 0.015 0.001 PHE L 59 TRP 0.005 0.001 TRP L 513 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 (28825) covalent geometry : angle 0.69049 / 0.38 (40274) hydrogen bonds : bond 0.06694 / 4.35 ( 1197) hydrogen bonds : angle 5.16904 / 3.66 ( 3225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 93 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.4587 (tmm) cc_final: 0.3855 (ptt) REVERT: C 112 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: F 95 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7994 (mtp85) REVERT: G 63 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9376 (mp) REVERT: A 50 GLU cc_start: 0.8510 (mp0) cc_final: 0.8053 (mp0) REVERT: B 84 MET cc_start: 0.8600 (mmm) cc_final: 0.7974 (mmm) REVERT: N 302 GLU cc_start: 0.4016 (OUTLIER) cc_final: 0.3568 (tm-30) REVERT: N 418 CYS cc_start: 0.6367 (OUTLIER) cc_final: 0.5972 (t) outliers start: 98 outliers final: 74 residues processed: 189 average time/residue: 0.1538 time to fit residues: 50.7886 Evaluate side-chains 170 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 91 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 262 optimal weight: 6.9990 chunk 270 optimal weight: 40.0000 chunk 225 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 254 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 112 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 101 ASN K 158 GLN L 359 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN N 484 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.095887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053207 restraints weight = 150891.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.054030 restraints weight = 61699.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053985 restraints weight = 37373.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054190 restraints weight = 28903.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.054278 restraints weight = 25245.613| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 28825 Z= 0.322 Angle : 0.751 10.666 40274 Z= 0.408 Chirality : 0.049 0.356 4632 Planarity : 0.005 0.075 4136 Dihedral : 27.313 173.954 6245 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.55 % Rotamer: Outliers : 4.98 % Allowed : 31.75 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.05 (0.16), residues: 2757 helix: 0.80 (0.15), residues: 1233 sheet: -1.99 (0.34), residues: 237 loop : -1.98 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 11 TYR 0.029 0.002 TYR F 88 PHE 0.018 0.002 PHE N 59 TRP 0.008 0.001 TRP N 276 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.32 (28825) covalent geometry : angle 0.75091 / 0.41 (40274) hydrogen bonds : bond 0.07389 / 4.86 ( 1197) hydrogen bonds : angle 5.43149 / 3.84 ( 3225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 90 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.4673 (tmm) cc_final: 0.3972 (ptt) REVERT: C 112 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: E 109 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9226 (tt) REVERT: F 95 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8047 (mtp85) REVERT: H 56 MET cc_start: 0.9297 (tpp) cc_final: 0.8919 (tpp) REVERT: A 50 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: A 68 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8724 (tp-100) REVERT: B 84 MET cc_start: 0.8768 (mmm) cc_final: 0.8051 (mmm) REVERT: N 212 MET cc_start: 0.1069 (ppp) cc_final: 0.0697 (ppp) REVERT: N 302 GLU cc_start: 0.3926 (OUTLIER) cc_final: 0.3504 (tm-30) outliers start: 114 outliers final: 89 residues processed: 200 average time/residue: 0.1551 time to fit residues: 53.5761 Evaluate side-chains 184 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 89 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 435 PHE Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 257 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain M residue 486 HIS Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 259 ILE Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 211 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 246 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 297 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 158 GLN K 416 GLN L 359 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.097123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054037 restraints weight = 149971.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054942 restraints weight = 60944.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.055431 restraints weight = 36877.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055357 restraints weight = 28150.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.055447 restraints weight = 24724.144| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28825 Z= 0.213 Angle : 0.670 12.647 40274 Z= 0.367 Chirality : 0.046 0.358 4632 Planarity : 0.004 0.071 4136 Dihedral : 27.290 176.095 6245 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 3.76 % Allowed : 32.75 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2757 helix: 0.99 (0.15), residues: 1233 sheet: -1.96 (0.34), residues: 243 loop : -1.92 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 11 TYR 0.035 0.001 TYR F 88 PHE 0.022 0.001 PHE K 99 TRP 0.007 0.001 TRP K 148 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (28825) covalent geometry : angle 0.66978 / 0.37 (40274) hydrogen bonds : bond 0.06586 / 4.27 ( 1197) hydrogen bonds : angle 5.15144 / 3.64 ( 3225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 95 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: -0.0617 (mmp) cc_final: -0.1053 (mmm) REVERT: L 115 MET cc_start: 0.4635 (tmm) cc_final: 0.3940 (ptt) REVERT: C 112 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: F 95 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8032 (mtp85) REVERT: H 56 MET cc_start: 0.9262 (tpp) cc_final: 0.8937 (tpp) REVERT: A 68 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8674 (tp-100) REVERT: B 84 MET cc_start: 0.8739 (mmm) cc_final: 0.8102 (mmm) REVERT: B 97 LEU cc_start: 0.9170 (tp) cc_final: 0.8864 (tt) REVERT: N 302 GLU cc_start: 0.4020 (OUTLIER) cc_final: 0.3516 (tm-30) REVERT: N 418 CYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6033 (t) outliers start: 86 outliers final: 72 residues processed: 180 average time/residue: 0.1581 time to fit residues: 48.9851 Evaluate side-chains 170 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 93 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 435 PHE Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 257 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain M residue 485 GLN Chi-restraints excluded: chain M residue 486 HIS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 245 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 255 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 299 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.094954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052747 restraints weight = 151217.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052544 restraints weight = 63641.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.052881 restraints weight = 38687.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053027 restraints weight = 29797.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.053080 restraints weight = 25901.243| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 28825 Z= 0.430 Angle : 0.844 12.911 40274 Z= 0.454 Chirality : 0.052 0.355 4632 Planarity : 0.005 0.079 4136 Dihedral : 27.366 173.583 6245 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.25 % Favored : 90.68 % Rotamer: Outliers : 4.24 % Allowed : 32.23 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.30 (0.16), residues: 2757 helix: 0.50 (0.15), residues: 1241 sheet: -2.14 (0.34), residues: 230 loop : -2.03 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.062 0.002 TYR F 88 PHE 0.033 0.002 PHE K 159 TRP 0.009 0.002 TRP K 148 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.43 (28825) covalent geometry : angle 0.84449 / 0.45 (40274) hydrogen bonds : bond 0.07950 / 5.27 ( 1197) hydrogen bonds : angle 5.72184 / 4.06 ( 3225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 88 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: -0.0487 (mmp) cc_final: -0.0919 (mmm) REVERT: L 115 MET cc_start: 0.4730 (tmm) cc_final: 0.4018 (ptt) REVERT: C 112 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: E 109 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9253 (tt) REVERT: F 95 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7962 (mtp85) REVERT: H 56 MET cc_start: 0.9304 (tpp) cc_final: 0.8793 (tpp) REVERT: A 50 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 68 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8784 (tp-100) REVERT: B 84 MET cc_start: 0.8824 (mmm) cc_final: 0.7988 (mmm) REVERT: N 210 MET cc_start: 0.5859 (mmm) cc_final: 0.5636 (ptt) REVERT: N 212 MET cc_start: 0.1136 (ppp) cc_final: 0.0735 (ppp) REVERT: N 302 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.3205 (tm-30) outliers start: 97 outliers final: 82 residues processed: 182 average time/residue: 0.1549 time to fit residues: 48.9524 Evaluate side-chains 176 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 88 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ARG Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain K residue 359 HIS Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 423 GLN Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 266 SER Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 435 PHE Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 482 ILE Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 257 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 319 SER Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain M residue 485 GLN Chi-restraints excluded: chain M residue 486 HIS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 157 CYS Chi-restraints excluded: chain N residue 283 THR Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 318 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 405 VAL Chi-restraints excluded: chain N residue 418 CYS Chi-restraints excluded: chain N residue 511 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 155 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 262 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 243 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 158 GLN L 359 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.098069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.055768 restraints weight = 149635.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055607 restraints weight = 60116.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056041 restraints weight = 36562.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056295 restraints weight = 28361.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.056423 restraints weight = 25689.663| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28825 Z= 0.150 Angle : 0.644 13.388 40274 Z= 0.355 Chirality : 0.045 0.372 4632 Planarity : 0.004 0.066 4136 Dihedral : 27.290 178.614 6245 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 3.23 % Allowed : 33.45 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2757 helix: 1.01 (0.15), residues: 1240 sheet: -2.08 (0.33), residues: 245 loop : -1.89 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 11 TYR 0.036 0.001 TYR F 88 PHE 0.022 0.001 PHE K 99 TRP 0.007 0.001 TRP L 513 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (28825) covalent geometry : angle 0.64395 / 0.35 (40274) hydrogen bonds : bond 0.06185 / 3.97 ( 1197) hydrogen bonds : angle 5.01595 / 3.54 ( 3225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10850.14 seconds wall clock time: 185 minutes 29.83 seconds (11129.83 seconds total)