Starting phenix.real_space_refine on Sun Aug 9 00:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7s_36047/08_2026/8j7s_36047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7s_36047/08_2026/8j7s_36047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2026/8j7s_36047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2026/8j7s_36047.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2026/8j7s_36047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2026/8j7s_36047.cif" } resolution = 2.84 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= -0.001 sd= 0.036 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 163 5.49 5 S 92 5.16 5 C 20019 2.51 5 N 5322 2.21 5 O 6216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3634 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3479 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3636 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3475 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "H" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "I" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3633 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "J" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3461 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3629 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3472 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "P" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N PHE A 238 " occ=0.23 ... (9 atoms not shown) pdb=" CZ PHE A 238 " occ=0.02 residue: pdb=" N GLY A 239 " occ=0.32 ... (2 atoms not shown) pdb=" O GLY A 239 " occ=0.20 residue: pdb=" N MET B 193 " occ=0.66 ... (6 atoms not shown) pdb=" CE MET B 193 " occ=0.35 residue: pdb=" N PRO B 195 " occ=0.13 ... (5 atoms not shown) pdb=" CD PRO B 195 " occ=0.77 residue: pdb=" N ASP B 199 " occ=0.47 ... (6 atoms not shown) pdb=" OD2 ASP B 199 " occ=0.87 residue: pdb=" N GLU B 296 " occ=0.63 ... (7 atoms not shown) pdb=" OE2 GLU B 296 " occ=0.57 residue: pdb=" N ASP B 346 " occ=0.92 ... (6 atoms not shown) pdb=" OD2 ASP B 346 " occ=0.55 residue: pdb=" N GLY B 396 " occ=0.26 ... (2 atoms not shown) pdb=" O GLY B 396 " occ=0.38 residue: pdb=" N GLY E 102 " occ=0.54 ... (2 atoms not shown) pdb=" O GLY E 102 " occ=0.07 residue: pdb=" N ALA E 237 " occ=0.11 ... (3 atoms not shown) pdb=" CB ALA E 237 " occ=0.21 residue: pdb=" N GLY E 239 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY E 239 " occ=0.74 residue: pdb=" N SER F 250 " occ=0.67 ... (4 atoms not shown) pdb=" OG SER F 250 " occ=0.09 ... (remaining 4 not shown) Time building chain proxies: 5.09, per 1000 atoms: 0.16 Number of scatterers: 31812 At special positions: 0 Unit cell: (134.662, 171.291, 225.156, 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 92 16.00 P 163 15.00 O 6216 8.00 N 5322 7.00 C 20019 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: 2.46 Conformation dependent library (CDL) restraints added in 920.7 milliseconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6640 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 36 sheets defined 35.4% alpha, 14.5% beta 58 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.652A pdb=" N ILE A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 110 through 131 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.520A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.687A pdb=" N GLY B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.057A pdb=" N PHE B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.109A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.664A pdb=" N MET B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.596A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.559A pdb=" N GLY E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.661A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 131 Processing helix chain 'E' and resid 206 through 214 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 331 through 351 removed outlier: 4.239A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 376 removed outlier: 3.614A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 Processing helix chain 'E' and resid 477 through 491 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 146 through 158 removed outlier: 4.268A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.007A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 257 through 279 removed outlier: 3.753A pdb=" N LYS F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 365 Processing helix chain 'F' and resid 369 through 385 removed outlier: 3.662A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 31 removed outlier: 3.615A pdb=" N GLY I 26 " --> pdb=" O ASP I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 62 removed outlier: 3.897A pdb=" N LYS I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 83 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.555A pdb=" N PHE I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR I 106 " --> pdb=" O GLY I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 131 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 248 through 264 Processing helix chain 'I' and resid 331 through 351 removed outlier: 3.685A pdb=" N GLN I 349 " --> pdb=" O SER I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.729A pdb=" N VAL I 376 " --> pdb=" O ALA I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 462 Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.578A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'J' and resid 14 through 29 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 71 through 89 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 123 through 139 Processing helix chain 'J' and resid 149 through 157 removed outlier: 4.024A pdb=" N LEU J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.769A pdb=" N GLU J 202 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.786A pdb=" N THR J 230 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 231 " --> pdb=" O PRO J 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 227 through 231' Processing helix chain 'J' and resid 257 through 277 Processing helix chain 'J' and resid 353 through 365 Processing helix chain 'J' and resid 369 through 384 removed outlier: 3.512A pdb=" N TRP J 373 " --> pdb=" O TRP J 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 22 through 30 Processing helix chain 'M' and resid 46 through 60 Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 87 through 89 No H-bonds generated for 'chain 'M' and resid 87 through 89' Processing helix chain 'M' and resid 97 through 106 removed outlier: 3.819A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 131 removed outlier: 3.784A pdb=" N THR M 114 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 213 Processing helix chain 'M' and resid 226 through 230 Processing helix chain 'M' and resid 248 through 264 Processing helix chain 'M' and resid 331 through 351 removed outlier: 3.708A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 376 Processing helix chain 'M' and resid 427 through 430 Processing helix chain 'M' and resid 451 through 463 Processing helix chain 'M' and resid 477 through 491 removed outlier: 3.533A pdb=" N THR M 491 " --> pdb=" O GLY M 487 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 Processing helix chain 'N' and resid 14 through 28 Processing helix chain 'N' and resid 45 through 56 Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 123 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.144A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 removed outlier: 3.585A pdb=" N GLU N 231 " --> pdb=" O PRO N 228 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR N 233 " --> pdb=" O THR N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 278 removed outlier: 3.603A pdb=" N CYS N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS N 262 " --> pdb=" O ASN N 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG N 263 " --> pdb=" O ALA N 259 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 366 removed outlier: 3.600A pdb=" N LYS N 366 " --> pdb=" O ARG N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 384 removed outlier: 3.798A pdb=" N TRP N 373 " --> pdb=" O TRP N 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.337A pdb=" N LYS A 2 " --> pdb=" O LYS B 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 4.925A pdb=" N VAL A 412 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 419 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 417 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 443 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.439A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.753A pdb=" N THR A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.571A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 179 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 175 through 179 current: chain 'B' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 291 through 294 current: chain 'B' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 334 through 344 current: chain 'B' and resid 400 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 3 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 3 current: chain 'F' and resid 169 through 179 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 291 through 294 current: chain 'F' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 334 through 344 current: chain 'F' and resid 400 through 412 Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 6 current: chain 'E' and resid 297 through 305 removed outlier: 3.751A pdb=" N LEU E 305 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 312 " --> pdb=" O LEU E 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 312 through 313 current: chain 'E' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 389 current: chain 'E' and resid 417 through 420 Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.534A pdb=" N GLN E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 94 through 95 removed outlier: 7.863A pdb=" N LYS E 94 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL E 43 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 141 " --> pdb=" O PHE E 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 425 through 426 Processing sheet with id=AB6, first strand: chain 'F' and resid 32 through 33 removed outlier: 7.115A pdb=" N LYS F 4 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE F 60 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 6 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU F 62 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER F 8 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER F 64 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 208 through 209 Processing sheet with id=AB8, first strand: chain 'I' and resid 2 through 3 removed outlier: 5.800A pdb=" N LYS I 2 " --> pdb=" O LYS J 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 5 through 6 current: chain 'I' and resid 297 through 305 removed outlier: 3.631A pdb=" N VAL I 312 " --> pdb=" O LEU I 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 312 through 313 current: chain 'I' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 382 through 389 current: chain 'I' and resid 417 through 420 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.544A pdb=" N LYS I 270 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 95 removed outlier: 6.044A pdb=" N GLY I 42 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 142 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE I 44 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP I 139 " --> pdb=" O GLN I 222 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE I 224 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL I 141 " --> pdb=" O PHE I 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 425 through 426 removed outlier: 3.579A pdb=" N THR I 431 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 31 through 33 removed outlier: 6.997A pdb=" N LYS J 4 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU J 61 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE J 6 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL J 63 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER J 8 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ILE J 95 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE J 60 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AC6, first strand: chain 'J' and resid 208 through 209 removed outlier: 4.096A pdb=" N VAL J 208 " --> pdb=" O CYS J 215 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS J 215 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 283 through 286 Processing sheet with id=AC8, first strand: chain 'J' and resid 390 through 394 Processing sheet with id=AC9, first strand: chain 'M' and resid 2 through 3 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 3 current: chain 'N' and resid 169 through 179 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 169 through 179 current: chain 'N' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 334 through 344 current: chain 'N' and resid 400 through 412 Processing sheet with id=AD1, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.619A pdb=" N GLN M 18 " --> pdb=" O PHE M 14 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 91 through 95 removed outlier: 7.132A pdb=" N SER M 41 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS M 94 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL M 43 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL M 141 " --> pdb=" O PHE M 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 278 through 287 removed outlier: 3.614A pdb=" N VAL M 312 " --> pdb=" O LEU M 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 312 through 313 current: chain 'M' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 389 current: chain 'M' and resid 441 through 447 Processing sheet with id=AD5, first strand: chain 'M' and resid 425 through 426 removed outlier: 3.670A pdb=" N THR M 431 " --> pdb=" O VAL M 426 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 32 through 33 removed outlier: 6.300A pdb=" N ILE N 5 " --> pdb=" O TRP N 33 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS N 4 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU N 61 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE N 6 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL N 63 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER N 8 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE N 95 " --> pdb=" O CYS N 58 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE N 60 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU N 97 " --> pdb=" O PHE N 60 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU N 62 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 164 through 165 Processing sheet with id=AD8, first strand: chain 'N' and resid 208 through 209 Processing sheet with id=AD9, first strand: chain 'N' and resid 283 through 286 996 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 3.04 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: 9154 1.34 - 1.46: 7889 1.46 - 1.58: 15426 1.58 - 1.70: 319 1.70 - 1.82: 140 Bond restraints: 32928 Sorted by residual: bond pdb=" CB PRO M 378 " pdb=" CG PRO M 378 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.21e+01 bond pdb=" C3' DA L 17 " pdb=" C2' DA L 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.26e+00 bond pdb=" C3' DA P 19 " pdb=" C2' DA P 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DG L 18 " pdb=" C2' DG L 18 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.84e+00 bond pdb=" C3' DA L 14 " pdb=" C2' DA L 14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.43e+00 ... (remaining 32923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 44886 2.94 - 5.88: 286 5.88 - 8.83: 43 8.83 - 11.77: 8 11.77 - 14.71: 5 Bond angle restraints: 45228 Sorted by residual: angle pdb=" CA PRO M 378 " pdb=" N PRO M 378 " pdb=" CD PRO M 378 " ideal model delta sigma weight residual 112.00 97.29 14.71 1.40e+00 5.10e-01 1.10e+02 angle pdb=" C1' U O 15 " pdb=" N1 U O 15 " pdb=" C2 U O 15 " ideal model delta sigma weight residual 117.70 123.78 -6.08 1.20e+00 6.94e-01 2.57e+01 angle pdb=" N1 U O 15 " pdb=" C2 U O 15 " pdb=" O2 U O 15 " ideal model delta sigma weight residual 122.80 126.08 -3.28 7.00e-01 2.04e+00 2.20e+01 angle pdb=" O2 U O 15 " pdb=" C2 U O 15 " pdb=" N3 U O 15 " ideal model delta sigma weight residual 122.20 118.99 3.21 7.00e-01 2.04e+00 2.10e+01 angle pdb=" O2 U C 15 " pdb=" C2 U C 15 " pdb=" N3 U C 15 " ideal model delta sigma weight residual 122.20 119.13 3.07 7.00e-01 2.04e+00 1.93e+01 ... (remaining 45223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 18175 33.89 - 67.78: 1284 67.78 - 101.66: 77 101.66 - 135.55: 1 135.55 - 169.44: 11 Dihedral angle restraints: 19548 sinusoidal: 9278 harmonic: 10270 Sorted by residual: dihedral pdb=" O4' U K 15 " pdb=" C1' U K 15 " pdb=" N1 U K 15 " pdb=" C2 U K 15 " ideal model delta sinusoidal sigma weight residual -160.00 9.44 -169.44 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U C 15 " pdb=" C1' U C 15 " pdb=" N1 U C 15 " pdb=" C2 U C 15 " ideal model delta sinusoidal sigma weight residual -160.00 6.92 -166.92 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U G 15 " pdb=" C1' U G 15 " pdb=" N1 U G 15 " pdb=" C2 U G 15 " ideal model delta sinusoidal sigma weight residual 200.00 44.25 155.75 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 19545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4129 0.059 - 0.117: 706 0.117 - 0.176: 137 0.176 - 0.234: 6 0.234 - 0.293: 2 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CG LEU J 264 " pdb=" CB LEU J 264 " pdb=" CD1 LEU J 264 " pdb=" CD2 LEU J 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE N 323 " pdb=" CA ILE N 323 " pdb=" CG1 ILE N 323 " pdb=" CG2 ILE N 323 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.60 -2.82 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4977 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 377 " -0.085 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO M 378 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO M 378 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 378 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 392 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO E 393 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 393 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 393 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 181 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 182 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.034 5.00e-02 4.00e+02 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1649 2.72 - 3.26: 30702 3.26 - 3.81: 54655 3.81 - 4.35: 67581 4.35 - 4.90: 109555 Nonbonded interactions: 264142 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" O TYR J 233 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR N 221 " pdb=" O TYR N 233 " model vdw 2.197 3.040 nonbonded pdb=" OE2 GLU J 281 " pdb=" OH TYR J 383 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR E 463 " pdb=" O ASP E 474 " model vdw 2.216 3.040 nonbonded pdb=" N GLU E 99 " pdb=" OE1 GLU E 99 " model vdw 2.218 3.120 ... (remaining 264137 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 1 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 321 or (resi \ d 322 and (name N or name CA or name C or name O or name CB )) or resid 323 thro \ ugh 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) o \ r resid 401 through 506)) selection = (chain 'E' and (resid 1 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 257 or (resid 258 through 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 321 or (resid 322 and (name N or name CA or name C or name O or \ name CB )) or resid 323 through 399 or (resid 400 and (name N or name CA or name \ C or name O or name CB )) or resid 401 through 506)) selection = (chain 'I' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 257 or (resid 258 through 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 321 or (resid 322 and (name N or name CA or name C or name O or name \ CB )) or resid 323 through 399 or (resid 400 and (name N or name CA or name C o \ r name O or name CB )) or resid 401 through 506)) selection = (chain 'M' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 257 or (resid 25 \ 8 through 260 and (name N or name CA or name C or name O or name CB )) or resid \ 261 through 308 or (resid 309 and (name N or name CA or name C or name O or name \ CB )) or resid 310 through 506)) } ncs_group { reference = (chain 'B' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 108 or (resid 109 and (name N or \ name CA or name C or name O or name CB )) or resid 110 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 64 or (resid 165 and (name N or name CA or name C or name O or name CB )) or res \ id 166 through 220 or (resid 221 and (name N or name CA or name C or name O or n \ ame CB )) or resid 222 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 370 or (resid 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 415 or (resid 416 \ and (name N or name CA or name C or name O or name CB )) or resid 417 through 4 \ 18)) selection = (chain 'F' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 99 or (resid 100 and (name N or nam \ e CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 125 \ or (resid 126 and (name N or name CA or name C or name O or name CB )) or resid \ 127 through 147 or (resid 148 and (name N or name CA or name C or name O or name \ CB )) or resid 149 through 164 or (resid 165 and (name N or name CA or name C o \ r name O or name CB )) or resid 166 through 316 or (resid 317 and (name N or nam \ e CA or name C or name O or name CB )) or resid 318 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 415 \ or (resid 416 and (name N or name CA or name C or name O or name CB )) or resid \ 417 through 418)) selection = (chain 'J' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 220 or (resid 221 \ and (name N or name CA or name C or name O or name CB )) or resid 222 through 3 \ 16 or (resid 317 and (name N or name CA or name C or name O or name CB )) or res \ id 318 through 370 or (resid 371 and (name N or name CA or name C or name O or n \ ame CB )) or resid 372 through 418)) selection = (chain 'N' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 125 or (resid 126 a \ nd (name N or name CA or name C or name O or name CB )) or resid 127 through 147 \ or (resid 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 164 or (resid 165 and (name N or name CA or name C or name O or nam \ e CB )) or resid 166 through 220 or (resid 221 and (name N or name CA or name C \ or name O or name CB )) or resid 222 through 415 or (resid 416 and (name N or na \ me CA or name C or name O or name CB )) or resid 417 through 418)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 8 through 27) selection = (chain 'L' and resid 8 through 27) } 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=0.01 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.450 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 0.174 32928 Z= 0.223 Angle : 0.697 14.711 45228 Z= 0.437 Chirality : 0.047 0.293 4980 Planarity : 0.004 0.119 5118 Dihedral : 20.376 169.439 12908 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 4.65 % Allowed : 29.35 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.12 (0.14), residues: 3464 helix: 0.84 (0.16), residues: 1132 sheet: -0.84 (0.21), residues: 590 loop : -1.83 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 257 TYR 0.020 0.001 TYR A 411 PHE 0.023 0.001 PHE N 17 TRP 0.039 0.001 TRP F 219 HIS 0.007 0.001 HIS N 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.22 (32928) covalent geometry : angle 0.69743 / 0.44 (45228) hydrogen bonds : bond 0.14421 / 9.20 ( 1136) hydrogen bonds : angle 6.03803 / 4.26 ( 3076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 294 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.8636 (m-80) cc_final: 0.8433 (m-10) REVERT: A 484 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7448 (OUTLIER) REVERT: B 167 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (mtmm) REVERT: B 227 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (mt) REVERT: F 309 MET cc_start: 0.5347 (tmm) cc_final: 0.5113 (tmm) REVERT: M 399 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6652 (p) REVERT: N 223 PHE cc_start: 0.4722 (m-80) cc_final: 0.4437 (m-10) outliers start: 143 outliers final: 74 residues processed: 424 average time/residue: 0.5097 time to fit residues: 264.4350 Evaluate side-chains 249 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 413 ASN Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 232 ARG Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 415 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 399 THR Chi-restraints excluded: chain M residue 422 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 414 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 129 ASN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 HIS ** N 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.085608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.066952 restraints weight = 142851.121| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.01 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 355 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1098 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32928 Z= 0.193 Angle : 0.688 11.120 45228 Z= 0.366 Chirality : 0.044 0.352 4980 Planarity : 0.004 0.062 5118 Dihedral : 18.779 169.733 6021 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 6.12 % Allowed : 27.53 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.01 (0.14), residues: 3464 helix: 0.90 (0.15), residues: 1160 sheet: -0.88 (0.21), residues: 604 loop : -1.73 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 257 TYR 0.023 0.001 TYR J 221 PHE 0.019 0.002 PHE A 304 TRP 0.026 0.001 TRP B 219 HIS 0.014 0.001 HIS J 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (32928) covalent geometry : angle 0.68784 / 0.37 (45228) hydrogen bonds : bond 0.04885 / 3.26 ( 1136) hydrogen bonds : angle 5.04019 / 3.56 ( 3076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 191 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9156 (m-30) cc_final: 0.8918 (m-30) REVERT: A 85 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8715 (mtmp) REVERT: B 86 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8781 (mtmm) REVERT: B 183 GLU cc_start: 0.9414 (pm20) cc_final: 0.9183 (pm20) REVERT: B 193 MET cc_start: 0.6464 (tpp) cc_final: 0.6194 (tpt) REVERT: B 205 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8232 (t80) REVERT: B 295 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7421 (mt) REVERT: B 301 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8113 (pp20) REVERT: B 309 MET cc_start: 0.7646 (tmm) cc_final: 0.7410 (tmm) REVERT: E 118 VAL cc_start: 0.9278 (t) cc_final: 0.8961 (p) REVERT: E 207 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8328 (t-170) REVERT: E 304 PHE cc_start: 0.8115 (t80) cc_final: 0.7870 (t80) REVERT: E 403 TYR cc_start: 0.6927 (m-10) cc_final: 0.6649 (m-80) REVERT: F 132 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9178 (mp) REVERT: F 133 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8776 (mm-30) REVERT: I 85 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8704 (mmmm) REVERT: I 255 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8608 (p) REVERT: J 4 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9040 (mptt) REVERT: J 313 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7657 (mmmt) REVERT: J 384 LEU cc_start: 0.8905 (pt) cc_final: 0.8338 (tp) REVERT: M 85 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8680 (mtpp) REVERT: N 335 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8577 (tm) REVERT: N 393 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8522 (mm) outliers start: 188 outliers final: 66 residues processed: 364 average time/residue: 0.4770 time to fit residues: 214.7666 Evaluate side-chains 251 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 171 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 298 CYS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 232 ARG Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 321 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 227 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 HIS ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN M 468 ASN N 160 HIS N 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.073677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.055657 restraints weight = 144026.191| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.75 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1098 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1097 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32928 Z= 0.202 Angle : 0.675 20.278 45228 Z= 0.355 Chirality : 0.045 0.378 4980 Planarity : 0.004 0.059 5118 Dihedral : 18.776 171.286 5959 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 5.86 % Allowed : 28.02 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.01 (0.14), residues: 3464 helix: 0.91 (0.15), residues: 1164 sheet: -0.91 (0.22), residues: 604 loop : -1.73 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 19 TYR 0.025 0.001 TYR N 293 PHE 0.024 0.002 PHE N 181 TRP 0.015 0.001 TRP F 219 HIS 0.016 0.001 HIS N 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (32928) covalent geometry : angle 0.67526 / 0.35 (45228) hydrogen bonds : bond 0.04615 / 3.08 ( 1136) hydrogen bonds : angle 4.89963 / 3.46 ( 3076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 185 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9133 (m-30) cc_final: 0.8831 (m-30) REVERT: A 85 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8827 (mtmp) REVERT: A 348 GLU cc_start: 0.9673 (pp20) cc_final: 0.9441 (pp20) REVERT: A 352 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8704 (pm20) REVERT: B 86 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8786 (mtmm) REVERT: B 138 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5715 (mp10) REVERT: B 183 GLU cc_start: 0.9414 (pm20) cc_final: 0.9171 (pm20) REVERT: B 185 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9246 (tt) REVERT: B 193 MET cc_start: 0.6599 (tpp) cc_final: 0.6349 (tpt) REVERT: B 205 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8328 (t80) REVERT: B 295 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7455 (mt) REVERT: B 301 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8372 (pp20) REVERT: B 309 MET cc_start: 0.7222 (tmm) cc_final: 0.6936 (tmm) REVERT: B 323 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8792 (mm) REVERT: E 118 VAL cc_start: 0.9246 (t) cc_final: 0.8881 (p) REVERT: E 207 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.8341 (t-170) REVERT: F 129 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8665 (mmtm) REVERT: F 132 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9125 (mp) REVERT: F 133 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8763 (mm-30) REVERT: I 1 MET cc_start: 0.7244 (mmm) cc_final: 0.7039 (tpp) REVERT: I 74 MET cc_start: 0.8561 (pp-130) cc_final: 0.8150 (ppp) REVERT: I 85 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8582 (mmmm) REVERT: I 370 TRP cc_start: 0.8608 (OUTLIER) cc_final: 0.7793 (t60) REVERT: J 4 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8997 (mptt) REVERT: J 234 HIS cc_start: 0.8600 (p90) cc_final: 0.8288 (p90) REVERT: J 313 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7660 (mmmt) REVERT: J 384 LEU cc_start: 0.8872 (pt) cc_final: 0.8272 (tp) REVERT: M 57 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7426 (tm) REVERT: M 234 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: N 167 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8379 (tmmm) REVERT: N 335 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8794 (tm) outliers start: 180 outliers final: 71 residues processed: 349 average time/residue: 0.4732 time to fit residues: 204.5273 Evaluate side-chains 255 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 165 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 335 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 348 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 320 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS E 430 GLN F 357 GLN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN M 468 ASN N 160 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.072090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.054118 restraints weight = 145227.143| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.73 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1097 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1113 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32928 Z= 0.244 Angle : 0.694 15.433 45228 Z= 0.363 Chirality : 0.046 0.385 4980 Planarity : 0.004 0.061 5118 Dihedral : 18.844 173.121 5946 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.55 % Rotamer: Outliers : 6.02 % Allowed : 27.76 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3464 helix: 0.78 (0.15), residues: 1192 sheet: -0.79 (0.23), residues: 560 loop : -1.77 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 19 TYR 0.019 0.001 TYR N 293 PHE 0.023 0.002 PHE A 304 TRP 0.015 0.002 TRP E 370 HIS 0.007 0.001 HIS E 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (32928) covalent geometry : angle 0.69356 / 0.36 (45228) hydrogen bonds : bond 0.04654 / 3.12 ( 1136) hydrogen bonds : angle 4.91272 / 3.47 ( 3076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 169 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9179 (m-30) cc_final: 0.8836 (m-30) REVERT: A 85 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8817 (mtmp) REVERT: A 352 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8774 (pm20) REVERT: B 86 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8721 (mtmm) REVERT: B 138 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5766 (mp10) REVERT: B 183 GLU cc_start: 0.9467 (pm20) cc_final: 0.9210 (pm20) REVERT: B 185 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9257 (tt) REVERT: B 193 MET cc_start: 0.6714 (tpp) cc_final: 0.6401 (tpt) REVERT: B 205 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 295 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7583 (mt) REVERT: B 309 MET cc_start: 0.7236 (tmm) cc_final: 0.7020 (tmm) REVERT: B 323 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8775 (mm) REVERT: E 118 VAL cc_start: 0.9246 (t) cc_final: 0.8872 (p) REVERT: E 207 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8371 (t-170) REVERT: E 430 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8249 (mm-40) REVERT: E 435 MET cc_start: 0.8140 (tpt) cc_final: 0.7831 (mtt) REVERT: F 126 ARG cc_start: 0.8835 (tpp-160) cc_final: 0.8550 (tpp-160) REVERT: F 129 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8618 (mmtm) REVERT: F 133 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8764 (mm-30) REVERT: F 193 MET cc_start: 0.7418 (tpp) cc_final: 0.6872 (tpp) REVERT: I 7 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7482 (pt) REVERT: I 85 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8578 (mmmm) REVERT: I 207 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8324 (t-170) REVERT: I 370 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.7841 (t60) REVERT: J 4 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8974 (mptt) REVERT: J 313 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7876 (tptp) REVERT: M 48 GLN cc_start: 0.8724 (mp10) cc_final: 0.8393 (pm20) REVERT: M 56 TYR cc_start: 0.8298 (t80) cc_final: 0.8063 (t80) REVERT: M 57 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7417 (tm) REVERT: M 234 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: M 444 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: N 167 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8405 (tmmm) REVERT: N 203 LEU cc_start: 0.7598 (mp) cc_final: 0.7186 (mm) REVERT: N 223 PHE cc_start: 0.6370 (m-10) cc_final: 0.6050 (m-10) outliers start: 185 outliers final: 86 residues processed: 344 average time/residue: 0.4230 time to fit residues: 185.1367 Evaluate side-chains 262 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 156 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 430 GLN Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 367 HIS Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 273 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN N 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.072684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.054617 restraints weight = 143563.861| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.77 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1113 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1165 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32928 Z= 0.157 Angle : 0.655 12.954 45228 Z= 0.340 Chirality : 0.045 0.410 4980 Planarity : 0.004 0.060 5118 Dihedral : 18.857 176.379 5941 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 5.43 % Allowed : 28.67 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.92 (0.14), residues: 3464 helix: 0.95 (0.15), residues: 1192 sheet: -0.87 (0.22), residues: 588 loop : -1.70 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 19 TYR 0.016 0.001 TYR J 221 PHE 0.020 0.001 PHE N 181 TRP 0.013 0.001 TRP E 370 HIS 0.011 0.001 HIS J 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (32928) covalent geometry : angle 0.65468 / 0.34 (45228) hydrogen bonds : bond 0.04156 / 2.79 ( 1136) hydrogen bonds : angle 4.76676 / 3.37 ( 3076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 173 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9194 (m-30) cc_final: 0.8776 (m-30) REVERT: A 40 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8420 (mttp) REVERT: A 303 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7352 (tmt) REVERT: A 352 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8795 (pm20) REVERT: B 86 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: B 138 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5816 (mp10) REVERT: B 183 GLU cc_start: 0.9482 (pm20) cc_final: 0.9208 (pm20) REVERT: B 193 MET cc_start: 0.6853 (tpp) cc_final: 0.6468 (tpt) REVERT: B 205 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8263 (t80) REVERT: B 295 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7559 (mt) REVERT: B 309 MET cc_start: 0.7110 (tmm) cc_final: 0.6893 (tmm) REVERT: B 323 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8787 (mm) REVERT: B 335 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8653 (tm) REVERT: E 118 VAL cc_start: 0.9255 (t) cc_final: 0.8877 (p) REVERT: E 207 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8395 (t-170) REVERT: F 129 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8581 (mmtm) REVERT: F 133 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8739 (mm-30) REVERT: F 193 MET cc_start: 0.7418 (tpp) cc_final: 0.7043 (tpp) REVERT: I 85 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8511 (mmmm) REVERT: I 370 TRP cc_start: 0.8646 (OUTLIER) cc_final: 0.7991 (t60) REVERT: I 485 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8066 (mttt) REVERT: J 4 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9029 (mptt) REVERT: J 266 VAL cc_start: 0.9303 (t) cc_final: 0.9052 (p) REVERT: J 313 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7820 (tptp) REVERT: M 48 GLN cc_start: 0.8768 (mp10) cc_final: 0.8445 (pm20) REVERT: M 234 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: M 444 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6492 (pp20) REVERT: N 193 MET cc_start: 0.7582 (tpt) cc_final: 0.7288 (tpt) REVERT: N 203 LEU cc_start: 0.7512 (mp) cc_final: 0.7193 (mm) outliers start: 167 outliers final: 80 residues processed: 328 average time/residue: 0.4476 time to fit residues: 183.8662 Evaluate side-chains 254 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 159 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 139 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 346 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.072405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.054275 restraints weight = 142797.252| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.99 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1165 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1213 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32928 Z= 0.159 Angle : 0.658 12.499 45228 Z= 0.341 Chirality : 0.045 0.492 4980 Planarity : 0.004 0.062 5118 Dihedral : 18.855 179.642 5935 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 5.43 % Allowed : 28.60 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3464 helix: 0.96 (0.15), residues: 1200 sheet: -0.68 (0.23), residues: 560 loop : -1.68 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 19 TYR 0.017 0.001 TYR F 225 PHE 0.016 0.001 PHE F 391 TRP 0.012 0.001 TRP I 254 HIS 0.008 0.001 HIS J 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (32928) covalent geometry : angle 0.65831 / 0.34 (45228) hydrogen bonds : bond 0.04082 / 2.75 ( 1136) hydrogen bonds : angle 4.75187 / 3.34 ( 3076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 175 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9211 (m-30) cc_final: 0.8769 (m-30) REVERT: A 40 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8432 (mttp) REVERT: A 352 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: A 484 ASP cc_start: 0.8751 (t70) cc_final: 0.8528 (OUTLIER) REVERT: B 138 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5728 (mp10) REVERT: B 183 GLU cc_start: 0.9476 (pm20) cc_final: 0.9199 (pm20) REVERT: B 193 MET cc_start: 0.7018 (tpp) cc_final: 0.6514 (tpt) REVERT: B 205 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 295 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7591 (mt) REVERT: B 309 MET cc_start: 0.7169 (tmm) cc_final: 0.6944 (tmm) REVERT: B 323 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 335 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8628 (tm) REVERT: E 118 VAL cc_start: 0.9251 (t) cc_final: 0.8876 (p) REVERT: E 207 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8376 (t-170) REVERT: E 435 MET cc_start: 0.8601 (mmm) cc_final: 0.8267 (mpp) REVERT: E 453 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9051 (mmmm) REVERT: F 133 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8814 (mm-30) REVERT: F 193 MET cc_start: 0.7336 (tpp) cc_final: 0.6761 (tpp) REVERT: I 85 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8481 (mmmm) REVERT: I 207 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8328 (t-170) REVERT: I 370 TRP cc_start: 0.8681 (OUTLIER) cc_final: 0.8027 (t60) REVERT: I 485 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8057 (mttt) REVERT: J 4 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9027 (mptt) REVERT: J 193 MET cc_start: 0.6526 (pmm) cc_final: 0.6322 (pmm) REVERT: J 266 VAL cc_start: 0.9280 (t) cc_final: 0.9042 (p) REVERT: M 7 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8523 (mm) REVERT: M 48 GLN cc_start: 0.8830 (mp10) cc_final: 0.8546 (pm20) REVERT: M 56 TYR cc_start: 0.8372 (t80) cc_final: 0.7881 (t80) REVERT: M 234 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: M 444 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6471 (pp20) REVERT: N 217 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8223 (m-80) outliers start: 167 outliers final: 81 residues processed: 329 average time/residue: 0.4478 time to fit residues: 187.0399 Evaluate side-chains 258 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 161 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 217 PHE Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 26 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 314 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.071591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.053372 restraints weight = 145045.341| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.75 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1213 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1286 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32928 Z= 0.202 Angle : 0.699 17.873 45228 Z= 0.355 Chirality : 0.045 0.386 4980 Planarity : 0.004 0.066 5118 Dihedral : 18.889 179.700 5930 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 4.98 % Allowed : 29.52 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.92 (0.14), residues: 3464 helix: 0.91 (0.15), residues: 1200 sheet: -0.77 (0.22), residues: 608 loop : -1.72 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 19 TYR 0.027 0.001 TYR F 225 PHE 0.030 0.002 PHE E 224 TRP 0.011 0.001 TRP E 370 HIS 0.007 0.001 HIS J 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (32928) covalent geometry : angle 0.69860 / 0.36 (45228) hydrogen bonds : bond 0.04237 / 2.85 ( 1136) hydrogen bonds : angle 4.80654 / 3.38 ( 3076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 164 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9180 (m-30) cc_final: 0.8748 (m-30) REVERT: A 40 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8368 (mttp) REVERT: A 85 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8868 (mtmp) REVERT: A 327 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: A 352 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8841 (pm20) REVERT: A 484 ASP cc_start: 0.8764 (t70) cc_final: 0.8547 (OUTLIER) REVERT: B 138 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5819 (mp10) REVERT: B 183 GLU cc_start: 0.9493 (pm20) cc_final: 0.9218 (pm20) REVERT: B 193 MET cc_start: 0.7221 (tpp) cc_final: 0.6871 (tpt) REVERT: B 201 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.9166 (mpt180) REVERT: B 295 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7545 (mt) REVERT: B 309 MET cc_start: 0.7166 (tmm) cc_final: 0.6954 (tmm) REVERT: B 323 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 335 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8625 (tm) REVERT: E 118 VAL cc_start: 0.9217 (t) cc_final: 0.8849 (p) REVERT: E 207 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8398 (t-170) REVERT: E 435 MET cc_start: 0.8658 (mmm) cc_final: 0.8230 (mtt) REVERT: E 453 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9084 (mmmm) REVERT: F 91 ASP cc_start: 0.7755 (t0) cc_final: 0.7363 (t0) REVERT: I 85 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8487 (mmmm) REVERT: I 370 TRP cc_start: 0.8701 (OUTLIER) cc_final: 0.8046 (t60) REVERT: J 4 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9003 (mptt) REVERT: M 48 GLN cc_start: 0.8907 (mp10) cc_final: 0.8637 (pm20) REVERT: M 56 TYR cc_start: 0.8422 (t80) cc_final: 0.7981 (t80) REVERT: M 234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: M 444 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6482 (pp20) outliers start: 153 outliers final: 88 residues processed: 305 average time/residue: 0.4526 time to fit residues: 174.9566 Evaluate side-chains 255 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 152 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 348 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 236 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 chunk 210 optimal weight: 0.3980 chunk 200 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.071206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.052935 restraints weight = 144950.055| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.75 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1286 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1335 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32928 Z= 0.206 Angle : 0.711 15.439 45228 Z= 0.360 Chirality : 0.045 0.389 4980 Planarity : 0.004 0.073 5118 Dihedral : 18.918 178.369 5928 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.16 % Favored : 92.73 % Rotamer: Outliers : 4.69 % Allowed : 29.91 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.96 (0.14), residues: 3464 helix: 0.90 (0.15), residues: 1192 sheet: -0.81 (0.21), residues: 608 loop : -1.75 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 19 TYR 0.015 0.001 TYR I 403 PHE 0.014 0.002 PHE M 358 TRP 0.013 0.001 TRP E 370 HIS 0.019 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (32928) covalent geometry : angle 0.71103 / 0.36 (45228) hydrogen bonds : bond 0.04273 / 2.86 ( 1136) hydrogen bonds : angle 4.81869 / 3.38 ( 3076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 158 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9175 (m-30) cc_final: 0.8714 (m-30) REVERT: A 40 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8193 (mttp) REVERT: A 327 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: A 352 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: A 484 ASP cc_start: 0.8780 (t70) cc_final: 0.8543 (OUTLIER) REVERT: B 138 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5594 (mp10) REVERT: B 183 GLU cc_start: 0.9511 (pm20) cc_final: 0.9218 (pm20) REVERT: B 193 MET cc_start: 0.7366 (tpp) cc_final: 0.6964 (tpt) REVERT: B 198 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7242 (t80) REVERT: B 201 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.9157 (mpt180) REVERT: B 295 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7425 (mt) REVERT: B 309 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6953 (tmm) REVERT: B 323 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8916 (mm) REVERT: B 335 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8676 (tm) REVERT: E 41 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7564 (p) REVERT: E 118 VAL cc_start: 0.9223 (t) cc_final: 0.8856 (p) REVERT: E 207 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8413 (t-170) REVERT: E 435 MET cc_start: 0.8732 (mmm) cc_final: 0.8309 (mtt) REVERT: E 453 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9084 (mmmm) REVERT: E 471 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6668 (pp) REVERT: F 133 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8728 (mm-30) REVERT: I 70 ILE cc_start: 0.9003 (mp) cc_final: 0.8436 (tt) REVERT: I 85 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8499 (mmmm) REVERT: I 207 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8546 (t-170) REVERT: I 278 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8759 (p) REVERT: I 370 TRP cc_start: 0.8702 (OUTLIER) cc_final: 0.8048 (t60) REVERT: I 457 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8781 (mtmm) REVERT: J 4 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8999 (mptt) REVERT: J 193 MET cc_start: 0.6827 (pmm) cc_final: 0.6488 (pmm) REVERT: J 395 MET cc_start: 0.7781 (pmm) cc_final: 0.2668 (tmt) REVERT: M 47 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9046 (mmtm) REVERT: M 48 GLN cc_start: 0.8905 (mp10) cc_final: 0.8635 (pm20) REVERT: M 234 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: M 444 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6447 (pp20) REVERT: N 193 MET cc_start: 0.7654 (tpt) cc_final: 0.7442 (tpt) REVERT: N 223 PHE cc_start: 0.6624 (m-10) cc_final: 0.6049 (m-10) outliers start: 144 outliers final: 85 residues processed: 291 average time/residue: 0.4641 time to fit residues: 170.8197 Evaluate side-chains 259 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 153 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 367 HIS Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 291 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 43 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 278 optimal weight: 0.8980 chunk 345 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 297 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.070309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.052117 restraints weight = 144644.578| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.03 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1335 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1385 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 32928 Z= 0.251 Angle : 0.744 15.525 45228 Z= 0.378 Chirality : 0.046 0.381 4980 Planarity : 0.004 0.076 5118 Dihedral : 18.974 178.292 5928 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.59 % Favored : 92.29 % Rotamer: Outliers : 4.49 % Allowed : 30.33 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.10 (0.14), residues: 3464 helix: 0.78 (0.15), residues: 1192 sheet: -1.00 (0.21), residues: 636 loop : -1.78 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 19 TYR 0.014 0.001 TYR F 225 PHE 0.034 0.002 PHE E 224 TRP 0.012 0.002 TRP E 370 HIS 0.007 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 (32928) covalent geometry : angle 0.74384 / 0.38 (45228) hydrogen bonds : bond 0.04509 / 3.02 ( 1136) hydrogen bonds : angle 4.90541 / 3.44 ( 3076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 153 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9204 (m-30) cc_final: 0.8716 (m-30) REVERT: A 85 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8816 (mtmp) REVERT: A 327 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: A 352 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: B 86 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8785 (ttmt) REVERT: B 183 GLU cc_start: 0.9527 (pm20) cc_final: 0.9203 (pm20) REVERT: B 193 MET cc_start: 0.7538 (tpp) cc_final: 0.7100 (tpt) REVERT: B 198 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7289 (t80) REVERT: B 201 ARG cc_start: 0.9549 (OUTLIER) cc_final: 0.9262 (mpt180) REVERT: B 295 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7806 (mt) REVERT: B 309 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: B 323 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8924 (mm) REVERT: B 335 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8720 (tm) REVERT: E 41 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7695 (p) REVERT: E 118 VAL cc_start: 0.9226 (t) cc_final: 0.8889 (p) REVERT: E 207 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8438 (t-170) REVERT: E 453 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9083 (mmmm) REVERT: E 471 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6770 (pp) REVERT: F 133 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8728 (mm-30) REVERT: F 193 MET cc_start: 0.7448 (mmm) cc_final: 0.6990 (tpt) REVERT: I 85 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8648 (mmmm) REVERT: I 207 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8598 (t-170) REVERT: I 278 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8784 (p) REVERT: I 370 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.8083 (t60) REVERT: I 457 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8788 (mtmm) REVERT: J 4 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9082 (mptt) REVERT: J 193 MET cc_start: 0.6805 (pmm) cc_final: 0.6465 (pmm) REVERT: M 47 LYS cc_start: 0.9393 (mmmm) cc_final: 0.8999 (mmtm) REVERT: M 48 GLN cc_start: 0.8900 (mp10) cc_final: 0.8649 (pm20) REVERT: M 234 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: M 444 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6440 (pp20) REVERT: N 83 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9122 (mmtm) REVERT: N 223 PHE cc_start: 0.6496 (m-10) cc_final: 0.5853 (m-10) outliers start: 138 outliers final: 84 residues processed: 279 average time/residue: 0.4855 time to fit residues: 169.2516 Evaluate side-chains 259 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 152 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 407 ARG Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 367 HIS Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 189 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 308 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 171 optimal weight: 5.9990 chunk 348 optimal weight: 8.9990 chunk 314 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** 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 = 0.4130 r_free = 0.4130 target = 0.071860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.053506 restraints weight = 143219.336| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.77 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1385 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1428 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32928 Z= 0.138 Angle : 0.711 15.026 45228 Z= 0.357 Chirality : 0.045 0.382 4980 Planarity : 0.004 0.085 5118 Dihedral : 18.937 174.856 5927 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 3.48 % Allowed : 31.47 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.94 (0.14), residues: 3464 helix: 0.96 (0.15), residues: 1192 sheet: -1.00 (0.21), residues: 616 loop : -1.69 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 19 TYR 0.015 0.001 TYR I 403 PHE 0.065 0.001 PHE N 380 TRP 0.014 0.001 TRP E 370 HIS 0.006 0.001 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (32928) covalent geometry : angle 0.71075 / 0.36 (45228) hydrogen bonds : bond 0.03993 / 2.68 ( 1136) hydrogen bonds : angle 4.75828 / 3.34 ( 3076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 164 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9152 (m-30) cc_final: 0.8691 (m-30) REVERT: A 40 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8428 (mmtp) REVERT: A 352 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: A 484 ASP cc_start: 0.8715 (t70) cc_final: 0.8469 (t0) REVERT: B 183 GLU cc_start: 0.9511 (pm20) cc_final: 0.9174 (pm20) REVERT: B 193 MET cc_start: 0.7462 (tpp) cc_final: 0.6998 (tpt) REVERT: B 198 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7328 (t80) REVERT: B 201 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.9197 (mpt180) REVERT: B 205 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8358 (t80) REVERT: B 295 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7616 (mt) REVERT: B 309 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6944 (tmm) REVERT: B 323 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8943 (mm) REVERT: B 395 MET cc_start: 0.9009 (tpt) cc_final: 0.8766 (tpp) REVERT: E 41 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7739 (p) REVERT: E 118 VAL cc_start: 0.9221 (t) cc_final: 0.8855 (p) REVERT: E 207 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.8466 (t-170) REVERT: E 435 MET cc_start: 0.8503 (mmm) cc_final: 0.8235 (mtt) REVERT: E 453 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9059 (mmmm) REVERT: E 471 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6664 (pp) REVERT: F 91 ASP cc_start: 0.7759 (t0) cc_final: 0.7348 (t0) REVERT: F 133 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8677 (mm-30) REVERT: I 85 LYS cc_start: 0.9124 (mmtp) cc_final: 0.8507 (mmmm) REVERT: I 207 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8606 (t-170) REVERT: I 278 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8854 (p) REVERT: I 370 TRP cc_start: 0.8671 (OUTLIER) cc_final: 0.8052 (t60) REVERT: J 4 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (mptt) REVERT: J 193 MET cc_start: 0.7036 (pmm) cc_final: 0.6661 (pmm) REVERT: J 234 HIS cc_start: 0.8614 (p90) cc_final: 0.8140 (p90) REVERT: J 394 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: J 395 MET cc_start: 0.7830 (pmm) cc_final: 0.2743 (tmt) REVERT: M 47 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9042 (mmtm) REVERT: M 48 GLN cc_start: 0.8894 (mp10) cc_final: 0.8645 (pm20) REVERT: M 56 TYR cc_start: 0.8447 (t80) cc_final: 0.8042 (t80) REVERT: M 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: M 258 THR cc_start: 0.9315 (m) cc_final: 0.8936 (t) REVERT: M 394 LEU cc_start: 0.8255 (tt) cc_final: 0.7948 (tp) REVERT: M 444 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6499 (pp20) REVERT: N 83 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9100 (mmtm) REVERT: N 137 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8620 (tmmt) REVERT: N 193 MET cc_start: 0.7578 (tpt) cc_final: 0.7207 (tpt) REVERT: N 223 PHE cc_start: 0.6669 (m-10) cc_final: 0.6076 (m-10) REVERT: N 229 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (ttpt) outliers start: 107 outliers final: 62 residues processed: 263 average time/residue: 0.4543 time to fit residues: 149.8902 Evaluate side-chains 239 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 156 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 394 GLU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 229 LYS Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 0.0070 chunk 182 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 chunk 344 optimal weight: 0.5980 chunk 102 optimal weight: 0.0980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.071535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.053227 restraints weight = 143482.669| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.77 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1428 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1468 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32928 Z= 0.157 Angle : 0.706 14.651 45228 Z= 0.354 Chirality : 0.045 0.391 4980 Planarity : 0.004 0.085 5118 Dihedral : 18.912 171.926 5926 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 3.19 % Allowed : 31.86 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.88 (0.14), residues: 3464 helix: 0.99 (0.15), residues: 1192 sheet: -0.86 (0.22), residues: 592 loop : -1.67 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 19 TYR 0.011 0.001 TYR N 293 PHE 0.030 0.001 PHE E 224 TRP 0.015 0.001 TRP M 370 HIS 0.006 0.001 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (32928) covalent geometry : angle 0.70608 / 0.35 (45228) hydrogen bonds : bond 0.04000 / 2.68 ( 1136) hydrogen bonds : angle 4.75446 / 3.34 ( 3076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10801.89 seconds wall clock time: 184 minutes 49.87 seconds (11089.87 seconds total)