Starting phenix.real_space_refine on Tue Aug 26 03:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozi_17310/08_2025/8ozi_17310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozi_17310/08_2025/8ozi_17310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ozi_17310/08_2025/8ozi_17310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozi_17310/08_2025/8ozi_17310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozi_17310/08_2025/8ozi_17310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozi_17310/08_2025/8ozi_17310.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. 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 136 5.49 5 S 96 5.16 5 C 20278 2.51 5 N 5314 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32092 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.21 Number of scatterers: 32092 At special positions: 0 Unit cell: (179.08, 208.12, 165.77, 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 96 16.00 P 136 15.00 O 6268 8.00 N 5314 7.00 C 20278 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: 3.03 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 27 sheets defined 40.5% alpha, 14.8% beta 25 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.657A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 removed outlier: 3.995A pdb=" N GLN A 70 " --> pdb=" O TYR A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.041A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.166A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.551A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 4.112A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 4.093A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.836A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.600A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.717A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.543A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.701A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.746A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.039A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 4.110A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.735A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 14 through 28 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.724A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 128 " --> pdb=" O TRP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.466A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 224 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.616A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.885A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 353 through 366 Processing helix chain 'C' and resid 369 through 384 removed outlier: 4.652A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 23 through 31 Processing helix chain 'D' and resid 46 through 62 removed outlier: 3.605A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.605A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.774A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 230 through 234 removed outlier: 4.133A pdb=" N ASP D 233 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 331 through 351 removed outlier: 4.154A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.773A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.598A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.590A pdb=" N TYR D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 28 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.542A pdb=" N GLU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 104 through 108 removed outlier: 4.054A pdb=" N ILE E 108 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.713A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 158 removed outlier: 4.145A pdb=" N SER E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.632A pdb=" N GLU E 202 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 203 " --> pdb=" O VAL E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.580A pdb=" N GLU E 231 " --> pdb=" O PRO E 228 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR E 233 " --> pdb=" O THR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.667A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 384 removed outlier: 3.721A pdb=" N THR E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 31 Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.522A pdb=" N LYS F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 109 through 131 removed outlier: 3.689A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 removed outlier: 3.779A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.607A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.664A pdb=" N ALA F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 351 removed outlier: 4.438A pdb=" N GLN F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.802A pdb=" N TRP F 370 " --> pdb=" O ASN F 366 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU F 375 " --> pdb=" O ASP F 371 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.549A pdb=" N LEU F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.553A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.589A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 29 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 71 through 89 Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.797A pdb=" N ILE G 108 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 114 Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.634A pdb=" N LEU G 128 " --> pdb=" O TRP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.549A pdb=" N GLU G 202 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 203 " --> pdb=" O VAL G 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 199 through 203' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.691A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR G 233 " --> pdb=" O THR G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 removed outlier: 3.670A pdb=" N THR G 238 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 249 Processing helix chain 'G' and resid 257 through 280 removed outlier: 3.941A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 353 through 366 Processing helix chain 'G' and resid 369 through 384 removed outlier: 4.106A pdb=" N THR G 375 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 22 through 31 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.672A pdb=" N LYS H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 83 Processing helix chain 'H' and resid 97 through 106 removed outlier: 3.603A pdb=" N PHE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 131 removed outlier: 4.212A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.850A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 Processing helix chain 'H' and resid 215 through 218 Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 248 through 265 Processing helix chain 'H' and resid 331 through 351 removed outlier: 3.536A pdb=" N TYR H 346 " --> pdb=" O SER H 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.579A pdb=" N LEU H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 491 removed outlier: 3.641A pdb=" N ASP H 484 " --> pdb=" O LEU H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.523A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.243A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 62 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 180 current: chain 'A' and resid 291 through 294 removed outlier: 7.354A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 415 removed outlier: 3.814A pdb=" N LYS B 2 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 413 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TYR B 6 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N SER A 415 " --> pdb=" O TYR B 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 6 current: chain 'B' and resid 297 through 305 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 311 through 315 current: chain 'B' and resid 384 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 384 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.641A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 removed outlier: 6.308A pdb=" N LYS C 4 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU C 61 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE C 6 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL C 63 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER C 8 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 178 current: chain 'C' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 291 through 294 current: chain 'C' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 334 through 344 current: chain 'C' and resid 400 through 415 removed outlier: 4.042A pdb=" N ASN C 413 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR D 6 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N SER C 415 " --> pdb=" O TYR D 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 6 current: chain 'D' and resid 297 through 305 removed outlier: 3.524A pdb=" N ALA D 300 " --> pdb=" O GLU D 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 311 through 316 current: chain 'D' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 382 through 389 current: chain 'D' and resid 417 through 420 Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 95 removed outlier: 7.178A pdb=" N SER D 41 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS D 94 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL D 43 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.074A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS E 4 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU E 61 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE E 6 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL E 63 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER E 8 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE E 95 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE E 60 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU E 97 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU E 62 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE E 118 " --> pdb=" O ILE E 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 165 through 180 current: chain 'E' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 291 through 294 current: chain 'E' and resid 317 through 328 removed outlier: 3.526A pdb=" N SER E 324 " --> pdb=" O SER E 338 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 415 removed outlier: 9.248A pdb=" N LYS F 2 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS E 409 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU F 4 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ASN E 413 " --> pdb=" O TYR F 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.587A pdb=" N HIS E 188 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 216 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 304 through 305 removed outlier: 3.547A pdb=" N PHE E 305 " --> pdb=" O THR E 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.552A pdb=" N ILE F 12 " --> pdb=" O CYS F 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.741A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 278 through 279 current: chain 'F' and resid 297 through 305 removed outlier: 3.792A pdb=" N ALA F 300 " --> pdb=" O GLU F 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 316 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 441 through 445 Processing sheet with id=AC2, first strand: chain 'G' and resid 32 through 33 removed outlier: 6.253A pdb=" N LYS G 4 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 61 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE G 6 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL G 63 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER G 8 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE G 118 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 165 through 172 removed outlier: 5.611A pdb=" N LYS G 167 " --> pdb=" O VAL G 414 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN G 413 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR H 6 " --> pdb=" O ASN G 413 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N SER G 415 " --> pdb=" O TYR H 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 301 removed outlier: 7.488A pdb=" N CYS H 298 " --> pdb=" O GLY H 318 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLY H 318 " --> pdb=" O CYS H 298 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA H 300 " --> pdb=" O GLU H 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 315 through 320 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AC4, first strand: chain 'G' and resid 283 through 286 removed outlier: 6.430A pdb=" N THR G 291 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY G 325 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER G 177 " --> pdb=" O SER G 404 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE G 402 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 393 " --> pdb=" O VAL G 401 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL G 403 " --> pdb=" O PHE G 391 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 208 through 210 Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 305 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AC8, first strand: chain 'H' and resid 92 through 95 removed outlier: 6.206A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 304 through 305 1042 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4931 1.31 - 1.43: 9816 1.43 - 1.56: 17993 1.56 - 1.69: 272 1.69 - 1.81: 148 Bond restraints: 33160 Sorted by residual: bond pdb=" C2B NAD C 501 " pdb=" C3B NAD C 501 " ideal model delta sigma weight residual 1.524 1.258 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C2B NAD G 501 " pdb=" C3B NAD G 501 " ideal model delta sigma weight residual 1.524 1.265 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C4D NAD C 501 " pdb=" O4D NAD C 501 " ideal model delta sigma weight residual 1.445 1.291 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C4D NAD G 501 " pdb=" O4D NAD G 501 " ideal model delta sigma weight residual 1.445 1.292 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C4B NAD G 501 " pdb=" C5B NAD G 501 " ideal model delta sigma weight residual 1.522 1.375 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 33155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 45213 3.90 - 7.80: 155 7.80 - 11.71: 16 11.71 - 15.61: 10 15.61 - 19.51: 8 Bond angle restraints: 45402 Sorted by residual: angle pdb=" C GLU F 352 " pdb=" N TYR F 353 " pdb=" CA TYR F 353 " ideal model delta sigma weight residual 120.60 131.06 -10.46 1.53e+00 4.27e-01 4.67e+01 angle pdb=" C4D NAD C 501 " pdb=" C3D NAD C 501 " pdb=" O3D NAD C 501 " ideal model delta sigma weight residual 108.31 127.82 -19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" C4D NAD G 501 " pdb=" C3D NAD G 501 " pdb=" O3D NAD G 501 " ideal model delta sigma weight residual 108.31 127.48 -19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" C1D NAD G 501 " pdb=" C2D NAD G 501 " pdb=" O2D NAD G 501 " ideal model delta sigma weight residual 110.62 128.49 -17.87 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1D NAD C 501 " pdb=" C2D NAD C 501 " pdb=" O2D NAD C 501 " ideal model delta sigma weight residual 110.62 128.42 -17.80 3.00e+00 1.11e-01 3.52e+01 ... (remaining 45397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 19183 33.80 - 67.60: 793 67.60 - 101.40: 54 101.40 - 135.20: 5 135.20 - 169.00: 15 Dihedral angle restraints: 20050 sinusoidal: 9542 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 7 " pdb=" C1' U N 7 " pdb=" N1 U N 7 " pdb=" C2 U N 7 " ideal model delta sinusoidal sigma weight residual 200.00 31.00 169.00 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U M 13 " pdb=" C1' U M 13 " pdb=" N1 U M 13 " pdb=" C2 U M 13 " ideal model delta sinusoidal sigma weight residual 200.00 36.83 163.17 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U K 13 " pdb=" C1' U K 13 " pdb=" N1 U K 13 " pdb=" C2 U K 13 " ideal model delta sinusoidal sigma weight residual 200.00 39.38 160.62 1 1.50e+01 4.44e-03 8.29e+01 ... (remaining 20047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.945: 4974 0.945 - 1.890: 0 1.890 - 2.835: 8 2.835 - 3.780: 0 3.780 - 4.726: 2 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1B NAD C 501 " pdb=" C2B NAD C 501 " pdb=" N9A NAD C 501 " pdb=" O4B NAD C 501 " both_signs ideal model delta sigma weight residual False 2.35 -2.38 4.73 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" C1B NAD G 501 " pdb=" C2B NAD G 501 " pdb=" N9A NAD G 501 " pdb=" O4B NAD G 501 " both_signs ideal model delta sigma weight residual False 2.35 -2.34 4.68 2.00e-01 2.50e+01 5.49e+02 chirality pdb=" C3D NAD G 501 " pdb=" C2D NAD G 501 " pdb=" C4D NAD G 501 " pdb=" O3D NAD G 501 " both_signs ideal model delta sigma weight residual False -2.73 -0.01 -2.72 2.00e-01 2.50e+01 1.85e+02 ... (remaining 4981 not shown) Planarity restraints: 5242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 72 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO H 73 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 73 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 73 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 318 " -0.043 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO D 319 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 392 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO H 393 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 393 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 393 " 0.035 5.00e-02 4.00e+02 ... (remaining 5239 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 869 2.68 - 3.23: 30738 3.23 - 3.79: 51545 3.79 - 4.34: 72113 4.34 - 4.90: 114634 Nonbonded interactions: 269899 Sorted by model distance: nonbonded pdb=" OG SER G 288 " pdb=" O2 U N 9 " model vdw 2.121 3.040 nonbonded pdb=" OG SER B 493 " pdb=" OD1 ASP B 495 " model vdw 2.124 3.040 nonbonded pdb=" OG SER C 288 " pdb=" O2 U K 9 " model vdw 2.147 3.040 nonbonded pdb=" O PRO H 500 " pdb=" OH TYR H 506 " model vdw 2.173 3.040 nonbonded pdb=" O LYS H 11 " pdb=" OG SER H 272 " model vdw 2.174 3.040 ... (remaining 269894 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 1 through 418) selection = chain 'E' selection = (chain 'G' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.820 Find NCS groups from input model: 0.610 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.005 0.266 33160 Z= 0.262 Angle : 0.771 19.512 45402 Z= 0.418 Chirality : 0.145 4.726 4984 Planarity : 0.005 0.070 5242 Dihedral : 17.635 168.998 13258 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.84 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3532 helix: 0.39 (0.15), residues: 1186 sheet: -1.04 (0.21), residues: 634 loop : -1.08 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 225 TYR 0.018 0.001 TYR G 285 PHE 0.026 0.002 PHE A 332 TRP 0.042 0.002 TRP F 370 HIS 0.006 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00535 (33160) covalent geometry : angle 0.77102 (45402) hydrogen bonds : bond 0.20974 ( 1092) hydrogen bonds : angle 8.20964 ( 2950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4158 (mtt) cc_final: 0.3457 (mmm) REVERT: B 122 ILE cc_start: 0.9008 (tt) cc_final: 0.8786 (tt) REVERT: B 148 TYR cc_start: 0.6610 (t80) cc_final: 0.5930 (t80) REVERT: C 295 LEU cc_start: 0.7648 (pt) cc_final: 0.7407 (tp) REVERT: D 74 MET cc_start: 0.7989 (ppp) cc_final: 0.7176 (ppp) REVERT: E 3 ASN cc_start: 0.7999 (p0) cc_final: 0.7739 (p0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1709 time to fit residues: 104.9846 Evaluate side-chains 250 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 226 HIS A 358 HIS A 364 GLN B 61 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 70 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN F 61 GLN F 302 GLN H 251 HIS H 430 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.139907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109622 restraints weight = 66020.277| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.76 r_work: 0.3521 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 33160 Z= 0.138 Angle : 0.604 9.364 45402 Z= 0.319 Chirality : 0.043 0.235 4984 Planarity : 0.005 0.063 5242 Dihedral : 18.472 179.673 5970 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.76 % Favored : 94.82 % Rotamer: Outliers : 0.88 % Allowed : 6.98 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.14), residues: 3532 helix: 0.68 (0.15), residues: 1210 sheet: -0.89 (0.21), residues: 610 loop : -1.13 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 225 TYR 0.023 0.001 TYR C 233 PHE 0.027 0.002 PHE A 223 TRP 0.022 0.001 TRP E 219 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00305 (33160) covalent geometry : angle 0.60440 (45402) hydrogen bonds : bond 0.05064 ( 1092) hydrogen bonds : angle 5.74458 ( 2950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 307 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.3789 (mtt) cc_final: 0.3282 (mmm) REVERT: B 122 ILE cc_start: 0.8891 (tt) cc_final: 0.8674 (tt) REVERT: C 295 LEU cc_start: 0.7789 (pt) cc_final: 0.7485 (tp) REVERT: D 430 GLN cc_start: 0.8656 (tp40) cc_final: 0.8239 (mm-40) REVERT: E 3 ASN cc_start: 0.8553 (p0) cc_final: 0.8213 (p0) REVERT: E 208 VAL cc_start: 0.7696 (t) cc_final: 0.7489 (p) REVERT: E 257 ARG cc_start: 0.5667 (mmm-85) cc_final: 0.5435 (mmm-85) REVERT: F 30 PHE cc_start: 0.8106 (m-80) cc_final: 0.7691 (m-80) REVERT: F 303 MET cc_start: 0.7977 (ttm) cc_final: 0.7722 (ttt) REVERT: F 476 GLU cc_start: 0.8258 (pt0) cc_final: 0.7602 (pt0) REVERT: G 367 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7973 (t0) REVERT: G 395 MET cc_start: 0.6662 (mmt) cc_final: 0.6409 (mmt) REVERT: H 101 ILE cc_start: 0.8754 (tt) cc_final: 0.8546 (tp) REVERT: H 387 THR cc_start: 0.8932 (t) cc_final: 0.8724 (m) REVERT: H 435 MET cc_start: 0.4835 (mmt) cc_final: 0.4531 (mmt) outliers start: 28 outliers final: 20 residues processed: 320 average time/residue: 0.1977 time to fit residues: 105.1307 Evaluate side-chains 272 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 120 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 317 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 226 HIS C 314 GLN D 135 ASN D 251 HIS ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 314 GLN E 370 ASN ** F 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 ASN H 329 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.132496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102071 restraints weight = 66405.917| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.73 r_work: 0.3401 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 33160 Z= 0.312 Angle : 0.734 11.337 45402 Z= 0.383 Chirality : 0.047 0.247 4984 Planarity : 0.006 0.070 5242 Dihedral : 18.768 179.053 5970 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.58 % Favored : 93.94 % Rotamer: Outliers : 2.13 % Allowed : 9.70 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3532 helix: 0.35 (0.15), residues: 1236 sheet: -1.06 (0.21), residues: 570 loop : -1.38 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 481 TYR 0.026 0.002 TYR F 148 PHE 0.025 0.002 PHE C 181 TRP 0.027 0.002 TRP E 219 HIS 0.007 0.002 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00725 (33160) covalent geometry : angle 0.73354 (45402) hydrogen bonds : bond 0.05556 ( 1092) hydrogen bonds : angle 5.70550 ( 2950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.3917 (mtt) cc_final: 0.3344 (mmm) REVERT: A 277 MET cc_start: 0.7226 (mmm) cc_final: 0.6887 (mmm) REVERT: B 12 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8620 (pt) REVERT: B 148 TYR cc_start: 0.6500 (t80) cc_final: 0.6192 (t80) REVERT: C 295 LEU cc_start: 0.7976 (pt) cc_final: 0.7498 (tp) REVERT: C 297 LYS cc_start: 0.6341 (mtpt) cc_final: 0.5779 (mtpt) REVERT: D 150 TYR cc_start: 0.7995 (m-80) cc_final: 0.7680 (m-80) REVERT: D 430 GLN cc_start: 0.8909 (tp40) cc_final: 0.8687 (tp40) REVERT: E 3 ASN cc_start: 0.8662 (p0) cc_final: 0.8264 (p0) REVERT: E 193 MET cc_start: 0.5069 (tpp) cc_final: 0.4783 (tpp) REVERT: E 208 VAL cc_start: 0.7624 (t) cc_final: 0.7423 (p) REVERT: F 74 MET cc_start: 0.6847 (ppp) cc_final: 0.6219 (ppp) REVERT: F 79 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: F 152 ARG cc_start: 0.8457 (ptt-90) cc_final: 0.8237 (ptt-90) REVERT: F 303 MET cc_start: 0.8125 (ttm) cc_final: 0.7859 (ttt) REVERT: F 358 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7647 (t80) REVERT: G 384 LEU cc_start: 0.8504 (mt) cc_final: 0.8118 (mt) REVERT: H 62 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8002 (ptmm) REVERT: H 248 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7987 (mp) outliers start: 68 outliers final: 48 residues processed: 305 average time/residue: 0.1891 time to fit residues: 96.5354 Evaluate side-chains 282 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 160 HIS Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 463 THR Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 119 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 351 optimal weight: 0.8980 chunk 321 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN D 322 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN G 258 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.136828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106555 restraints weight = 65430.209| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.73 r_work: 0.3480 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 33160 Z= 0.126 Angle : 0.574 8.318 45402 Z= 0.302 Chirality : 0.042 0.233 4984 Planarity : 0.005 0.064 5242 Dihedral : 18.522 179.246 5970 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.67 % Favored : 94.90 % Rotamer: Outliers : 1.60 % Allowed : 11.51 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3532 helix: 0.65 (0.15), residues: 1244 sheet: -1.16 (0.21), residues: 616 loop : -1.23 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 225 TYR 0.017 0.001 TYR H 425 PHE 0.022 0.001 PHE A 332 TRP 0.018 0.001 TRP E 219 HIS 0.004 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00287 (33160) covalent geometry : angle 0.57420 (45402) hydrogen bonds : bond 0.04338 ( 1092) hydrogen bonds : angle 5.29462 ( 2950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 285 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.3545 (mtt) cc_final: 0.3028 (mmm) REVERT: A 378 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7212 (tp) REVERT: B 1 MET cc_start: 0.4468 (mmp) cc_final: 0.4196 (mmp) REVERT: B 148 TYR cc_start: 0.6575 (t80) cc_final: 0.6175 (t80) REVERT: C 162 LYS cc_start: 0.4727 (mmpt) cc_final: 0.4431 (mmpt) REVERT: C 295 LEU cc_start: 0.7989 (pt) cc_final: 0.7573 (tp) REVERT: C 371 ASN cc_start: 0.8214 (m110) cc_final: 0.7715 (t0) REVERT: D 150 TYR cc_start: 0.7956 (m-80) cc_final: 0.7653 (m-80) REVERT: D 430 GLN cc_start: 0.8901 (tp40) cc_final: 0.8273 (mm-40) REVERT: E 3 ASN cc_start: 0.8591 (p0) cc_final: 0.8214 (p0) REVERT: E 136 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: E 157 ILE cc_start: 0.9253 (mm) cc_final: 0.9049 (mm) REVERT: E 208 VAL cc_start: 0.7633 (t) cc_final: 0.7414 (p) REVERT: F 79 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: F 100 ASP cc_start: 0.7858 (m-30) cc_final: 0.7543 (m-30) REVERT: F 303 MET cc_start: 0.8128 (ttm) cc_final: 0.7907 (ttt) REVERT: G 373 TRP cc_start: 0.8001 (m100) cc_final: 0.7670 (m100) outliers start: 51 outliers final: 32 residues processed: 318 average time/residue: 0.1891 time to fit residues: 100.4650 Evaluate side-chains 288 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 296 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 203 optimal weight: 0.0000 chunk 24 optimal weight: 8.9990 chunk 347 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN F 98 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.135843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105701 restraints weight = 65964.155| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.72 r_work: 0.3466 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33160 Z= 0.150 Angle : 0.577 8.779 45402 Z= 0.302 Chirality : 0.042 0.231 4984 Planarity : 0.005 0.066 5242 Dihedral : 18.454 179.722 5970 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.29 % Favored : 94.31 % Rotamer: Outliers : 1.91 % Allowed : 12.86 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3532 helix: 0.72 (0.15), residues: 1252 sheet: -1.13 (0.22), residues: 602 loop : -1.28 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 113 TYR 0.020 0.001 TYR G 293 PHE 0.021 0.001 PHE A 332 TRP 0.018 0.001 TRP E 219 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00346 (33160) covalent geometry : angle 0.57653 (45402) hydrogen bonds : bond 0.04311 ( 1092) hydrogen bonds : angle 5.19588 ( 2950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6693 (m100) cc_final: 0.5646 (m100) REVERT: A 193 MET cc_start: 0.3766 (mtt) cc_final: 0.3232 (mmm) REVERT: A 277 MET cc_start: 0.7119 (mmm) cc_final: 0.6601 (mmm) REVERT: B 1 MET cc_start: 0.4494 (mmp) cc_final: 0.4275 (mmp) REVERT: B 324 LYS cc_start: 0.7961 (tmtt) cc_final: 0.6964 (mttp) REVERT: C 219 TRP cc_start: 0.7119 (t60) cc_final: 0.6877 (t60) REVERT: C 286 GLU cc_start: 0.7387 (pt0) cc_final: 0.7101 (pm20) REVERT: C 295 LEU cc_start: 0.8016 (pt) cc_final: 0.7606 (tp) REVERT: C 371 ASN cc_start: 0.8143 (m110) cc_final: 0.7826 (t0) REVERT: D 117 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8579 (mm) REVERT: D 150 TYR cc_start: 0.8016 (m-80) cc_final: 0.7687 (m-10) REVERT: D 430 GLN cc_start: 0.8898 (tp40) cc_final: 0.8218 (mm-40) REVERT: E 3 ASN cc_start: 0.8611 (p0) cc_final: 0.8212 (p0) REVERT: E 136 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: E 157 ILE cc_start: 0.9241 (mm) cc_final: 0.9016 (mm) REVERT: E 193 MET cc_start: 0.5078 (tpp) cc_final: 0.4768 (tpp) REVERT: E 208 VAL cc_start: 0.7662 (t) cc_final: 0.7411 (p) REVERT: F 79 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: F 303 MET cc_start: 0.8189 (ttm) cc_final: 0.7866 (ttt) REVERT: F 325 ASN cc_start: 0.8690 (t0) cc_final: 0.8409 (t0) REVERT: F 435 MET cc_start: 0.6660 (mmt) cc_final: 0.6295 (mmt) REVERT: G 158 PHE cc_start: 0.6911 (t80) cc_final: 0.6140 (t80) REVERT: G 373 TRP cc_start: 0.8007 (m100) cc_final: 0.7629 (m100) REVERT: H 62 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7923 (ptmm) REVERT: H 352 GLU cc_start: 0.6724 (tp30) cc_final: 0.6489 (tp30) outliers start: 61 outliers final: 35 residues processed: 313 average time/residue: 0.1691 time to fit residues: 88.6924 Evaluate side-chains 284 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 333 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS B 207 HIS B 302 GLN ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.133763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103673 restraints weight = 65577.595| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.70 r_work: 0.3431 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33160 Z= 0.205 Angle : 0.612 9.272 45402 Z= 0.320 Chirality : 0.043 0.240 4984 Planarity : 0.005 0.069 5242 Dihedral : 18.492 179.859 5970 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.75 % Favored : 93.91 % Rotamer: Outliers : 2.19 % Allowed : 13.70 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.14), residues: 3532 helix: 0.65 (0.15), residues: 1252 sheet: -1.15 (0.22), residues: 586 loop : -1.37 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 257 TYR 0.025 0.002 TYR A 416 PHE 0.026 0.002 PHE A 332 TRP 0.018 0.001 TRP E 219 HIS 0.004 0.001 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00476 (33160) covalent geometry : angle 0.61208 (45402) hydrogen bonds : bond 0.04492 ( 1092) hydrogen bonds : angle 5.24233 ( 2950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 267 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6694 (m100) cc_final: 0.5563 (m100) REVERT: A 67 TYR cc_start: 0.8735 (m-80) cc_final: 0.8466 (m-80) REVERT: A 193 MET cc_start: 0.3735 (mtt) cc_final: 0.3204 (mmm) REVERT: A 307 LYS cc_start: 0.7584 (tmtt) cc_final: 0.7183 (mmtt) REVERT: B 12 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8567 (pt) REVERT: C 219 TRP cc_start: 0.7186 (t60) cc_final: 0.6955 (t60) REVERT: C 286 GLU cc_start: 0.7373 (pt0) cc_final: 0.6966 (pm20) REVERT: C 295 LEU cc_start: 0.8089 (pt) cc_final: 0.7635 (tp) REVERT: D 117 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8609 (mm) REVERT: D 150 TYR cc_start: 0.8028 (m-80) cc_final: 0.7726 (m-10) REVERT: D 430 GLN cc_start: 0.8947 (tp40) cc_final: 0.8152 (mm-40) REVERT: E 3 ASN cc_start: 0.8634 (p0) cc_final: 0.8216 (p0) REVERT: E 136 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: E 156 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: E 157 ILE cc_start: 0.9241 (mm) cc_final: 0.9033 (mm) REVERT: E 208 VAL cc_start: 0.7488 (t) cc_final: 0.7227 (p) REVERT: F 79 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: F 303 MET cc_start: 0.8212 (ttm) cc_final: 0.7902 (ttt) REVERT: G 158 PHE cc_start: 0.6931 (t80) cc_final: 0.6403 (t80) REVERT: H 62 LYS cc_start: 0.8432 (mtmt) cc_final: 0.7962 (ptmm) REVERT: H 352 GLU cc_start: 0.6710 (tp30) cc_final: 0.6409 (tp30) outliers start: 70 outliers final: 50 residues processed: 319 average time/residue: 0.1595 time to fit residues: 86.5361 Evaluate side-chains 305 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 163 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 0.0170 chunk 59 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 236 optimal weight: 0.0070 chunk 33 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 ASN D 205 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** G 138 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 = 0.4104 r_free = 0.4104 target = 0.139379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109662 restraints weight = 66223.955| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.68 r_work: 0.3542 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33160 Z= 0.113 Angle : 0.555 9.350 45402 Z= 0.292 Chirality : 0.042 0.225 4984 Planarity : 0.004 0.070 5242 Dihedral : 18.353 179.390 5970 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.07 % Favored : 94.73 % Rotamer: Outliers : 1.69 % Allowed : 14.61 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3532 helix: 0.91 (0.15), residues: 1240 sheet: -1.10 (0.22), residues: 602 loop : -1.27 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 152 TYR 0.020 0.001 TYR C 233 PHE 0.023 0.001 PHE A 332 TRP 0.016 0.001 TRP E 219 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00251 (33160) covalent geometry : angle 0.55491 (45402) hydrogen bonds : bond 0.03970 ( 1092) hydrogen bonds : angle 5.05131 ( 2950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6689 (m100) cc_final: 0.5534 (m100) REVERT: A 67 TYR cc_start: 0.8647 (m-80) cc_final: 0.8423 (m-80) REVERT: A 166 GLU cc_start: 0.7602 (tp30) cc_final: 0.6890 (tt0) REVERT: A 193 MET cc_start: 0.3685 (mtt) cc_final: 0.3172 (mmm) REVERT: B 12 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8560 (pt) REVERT: B 324 LYS cc_start: 0.7869 (tmtt) cc_final: 0.6933 (mttp) REVERT: C 219 TRP cc_start: 0.7260 (t60) cc_final: 0.6889 (t60) REVERT: C 286 GLU cc_start: 0.7310 (pt0) cc_final: 0.6953 (pm20) REVERT: C 295 LEU cc_start: 0.8054 (pt) cc_final: 0.7644 (tp) REVERT: C 411 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7531 (ttpp) REVERT: D 117 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8595 (mm) REVERT: D 150 TYR cc_start: 0.8021 (m-80) cc_final: 0.7680 (m-10) REVERT: D 430 GLN cc_start: 0.8916 (tp40) cc_final: 0.8323 (mm-40) REVERT: D 497 LYS cc_start: 0.8469 (mptt) cc_final: 0.8047 (mmtp) REVERT: E 3 ASN cc_start: 0.8549 (p0) cc_final: 0.8150 (p0) REVERT: E 136 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: E 156 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: E 157 ILE cc_start: 0.9174 (mm) cc_final: 0.8952 (mm) REVERT: E 208 VAL cc_start: 0.7616 (t) cc_final: 0.7349 (p) REVERT: E 395 MET cc_start: 0.5924 (mmm) cc_final: 0.5137 (mmm) REVERT: F 29 LEU cc_start: 0.9099 (tp) cc_final: 0.8759 (mt) REVERT: F 79 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: F 303 MET cc_start: 0.7939 (ttm) cc_final: 0.7724 (ttt) REVERT: F 435 MET cc_start: 0.6441 (mmt) cc_final: 0.6071 (mmt) REVERT: G 158 PHE cc_start: 0.6934 (t80) cc_final: 0.6358 (t80) REVERT: G 285 TYR cc_start: 0.6822 (t80) cc_final: 0.6346 (t80) REVERT: G 373 TRP cc_start: 0.8000 (m100) cc_final: 0.7666 (m100) REVERT: H 62 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8028 (ptmm) REVERT: H 352 GLU cc_start: 0.6755 (tp30) cc_final: 0.6462 (tp30) REVERT: H 411 TYR cc_start: 0.8052 (t80) cc_final: 0.7384 (t80) outliers start: 54 outliers final: 40 residues processed: 320 average time/residue: 0.1935 time to fit residues: 102.2503 Evaluate side-chains 298 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 192 TRP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 403 TYR Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 94 optimal weight: 5.9990 chunk 73 optimal weight: 0.0980 chunk 216 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 364 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.136108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106354 restraints weight = 66528.709| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.65 r_work: 0.3488 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33160 Z= 0.206 Angle : 0.616 10.335 45402 Z= 0.320 Chirality : 0.043 0.274 4984 Planarity : 0.005 0.075 5242 Dihedral : 18.391 179.529 5970 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 94.00 % Rotamer: Outliers : 2.35 % Allowed : 14.55 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3532 helix: 0.92 (0.15), residues: 1228 sheet: -1.13 (0.22), residues: 590 loop : -1.35 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 152 TYR 0.022 0.002 TYR A 416 PHE 0.024 0.002 PHE G 343 TRP 0.017 0.001 TRP E 219 HIS 0.010 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00478 (33160) covalent geometry : angle 0.61589 (45402) hydrogen bonds : bond 0.04346 ( 1092) hydrogen bonds : angle 5.14691 ( 2950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6554 (m100) cc_final: 0.5330 (m100) REVERT: A 67 TYR cc_start: 0.8718 (m-80) cc_final: 0.8480 (m-80) REVERT: A 166 GLU cc_start: 0.7650 (tp30) cc_final: 0.6870 (tt0) REVERT: A 193 MET cc_start: 0.3682 (mtt) cc_final: 0.3152 (mmm) REVERT: A 307 LYS cc_start: 0.7655 (tmtt) cc_final: 0.7215 (mmtt) REVERT: A 369 TRP cc_start: 0.4678 (m100) cc_final: 0.4442 (m-10) REVERT: B 12 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8566 (pt) REVERT: B 324 LYS cc_start: 0.7986 (tmtt) cc_final: 0.6982 (mttp) REVERT: C 219 TRP cc_start: 0.7314 (t60) cc_final: 0.6935 (t60) REVERT: C 286 GLU cc_start: 0.7337 (pt0) cc_final: 0.6936 (pm20) REVERT: C 295 LEU cc_start: 0.8101 (pt) cc_final: 0.7664 (tp) REVERT: D 117 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8640 (mm) REVERT: D 150 TYR cc_start: 0.8009 (m-80) cc_final: 0.7805 (m-10) REVERT: D 415 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: D 430 GLN cc_start: 0.8956 (tp40) cc_final: 0.8384 (mm-40) REVERT: D 497 LYS cc_start: 0.8500 (mptt) cc_final: 0.8083 (mmtp) REVERT: E 3 ASN cc_start: 0.8592 (p0) cc_final: 0.8193 (p0) REVERT: E 136 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: E 156 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: E 193 MET cc_start: 0.5425 (tpp) cc_final: 0.5208 (tpp) REVERT: E 208 VAL cc_start: 0.7581 (t) cc_final: 0.7288 (p) REVERT: F 29 LEU cc_start: 0.9109 (tp) cc_final: 0.8726 (mt) REVERT: F 79 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: F 303 MET cc_start: 0.8105 (ttm) cc_final: 0.7806 (ttt) REVERT: F 447 LYS cc_start: 0.7091 (tmtt) cc_final: 0.6868 (tttt) REVERT: G 158 PHE cc_start: 0.6892 (t80) cc_final: 0.6389 (t80) REVERT: G 285 TYR cc_start: 0.6855 (t80) cc_final: 0.6309 (t80) REVERT: G 319 TRP cc_start: 0.7529 (p-90) cc_final: 0.6716 (p-90) REVERT: H 62 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8169 (ptmm) REVERT: H 317 VAL cc_start: 0.8936 (t) cc_final: 0.8706 (t) outliers start: 75 outliers final: 51 residues processed: 316 average time/residue: 0.1853 time to fit residues: 99.0760 Evaluate side-chains 302 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 192 TRP Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 403 TYR Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 52 optimal weight: 4.9990 chunk 315 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 209 optimal weight: 0.9980 chunk 300 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 301 optimal weight: 0.0970 chunk 307 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS B 468 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** G 138 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 = 0.4071 r_free = 0.4071 target = 0.136881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107278 restraints weight = 65852.521| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.64 r_work: 0.3504 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33160 Z= 0.160 Angle : 0.593 10.290 45402 Z= 0.309 Chirality : 0.043 0.265 4984 Planarity : 0.005 0.077 5242 Dihedral : 18.363 179.725 5970 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.28 % Rotamer: Outliers : 1.88 % Allowed : 15.33 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3532 helix: 1.01 (0.15), residues: 1216 sheet: -1.15 (0.22), residues: 590 loop : -1.33 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 225 TYR 0.021 0.001 TYR G 293 PHE 0.024 0.001 PHE G 343 TRP 0.016 0.001 TRP E 219 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00371 (33160) covalent geometry : angle 0.59295 (45402) hydrogen bonds : bond 0.04151 ( 1092) hydrogen bonds : angle 5.11776 ( 2950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6551 (m100) cc_final: 0.5309 (m100) REVERT: A 67 TYR cc_start: 0.8707 (m-80) cc_final: 0.8483 (m-80) REVERT: A 166 GLU cc_start: 0.7614 (tp30) cc_final: 0.6847 (tt0) REVERT: A 193 MET cc_start: 0.3705 (mtt) cc_final: 0.3176 (mmm) REVERT: A 307 LYS cc_start: 0.7662 (tmtt) cc_final: 0.7214 (mmtt) REVERT: A 369 TRP cc_start: 0.4638 (m100) cc_final: 0.4424 (m-10) REVERT: B 12 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8526 (pt) REVERT: B 324 LYS cc_start: 0.7949 (tmtt) cc_final: 0.6968 (mttp) REVERT: C 219 TRP cc_start: 0.7296 (t60) cc_final: 0.6919 (t60) REVERT: C 286 GLU cc_start: 0.7326 (pt0) cc_final: 0.6914 (pm20) REVERT: C 295 LEU cc_start: 0.8118 (pt) cc_final: 0.7655 (tp) REVERT: C 411 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7565 (ttpp) REVERT: D 117 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8631 (mm) REVERT: D 150 TYR cc_start: 0.7989 (m-80) cc_final: 0.7763 (m-10) REVERT: D 430 GLN cc_start: 0.9000 (tp40) cc_final: 0.8485 (mm-40) REVERT: D 497 LYS cc_start: 0.8444 (mptt) cc_final: 0.8025 (mmtp) REVERT: E 3 ASN cc_start: 0.8582 (p0) cc_final: 0.8200 (p0) REVERT: E 136 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: E 156 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: E 193 MET cc_start: 0.5376 (tpp) cc_final: 0.5142 (tpp) REVERT: E 208 VAL cc_start: 0.7559 (t) cc_final: 0.7260 (p) REVERT: F 29 LEU cc_start: 0.9109 (tp) cc_final: 0.8701 (mt) REVERT: F 79 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: F 303 MET cc_start: 0.8073 (ttm) cc_final: 0.7794 (ttt) REVERT: G 158 PHE cc_start: 0.6890 (t80) cc_final: 0.6392 (t80) REVERT: G 285 TYR cc_start: 0.6794 (t80) cc_final: 0.6293 (t80) REVERT: G 319 TRP cc_start: 0.7531 (p-90) cc_final: 0.6677 (p-90) REVERT: G 373 TRP cc_start: 0.7911 (m100) cc_final: 0.7636 (m100) REVERT: H 62 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8085 (ptmm) REVERT: H 317 VAL cc_start: 0.8925 (t) cc_final: 0.8689 (t) REVERT: H 411 TYR cc_start: 0.8170 (t80) cc_final: 0.7245 (t80) REVERT: H 429 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6876 (tp) REVERT: H 471 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8343 (tp) outliers start: 60 outliers final: 45 residues processed: 306 average time/residue: 0.1836 time to fit residues: 94.2966 Evaluate side-chains 300 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 192 TRP Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 403 TYR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 471 ILE Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 168 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 213 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS B 468 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.107860 restraints weight = 66575.048| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.65 r_work: 0.3513 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33160 Z= 0.145 Angle : 0.582 9.922 45402 Z= 0.303 Chirality : 0.042 0.262 4984 Planarity : 0.005 0.078 5242 Dihedral : 18.318 179.020 5970 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 1.88 % Allowed : 15.27 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3532 helix: 1.07 (0.15), residues: 1214 sheet: -1.13 (0.22), residues: 592 loop : -1.33 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 225 TYR 0.027 0.001 TYR G 293 PHE 0.036 0.001 PHE G 343 TRP 0.016 0.001 TRP G 319 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00335 (33160) covalent geometry : angle 0.58213 (45402) hydrogen bonds : bond 0.04052 ( 1092) hydrogen bonds : angle 5.08182 ( 2950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TYR cc_start: 0.8686 (m-80) cc_final: 0.8467 (m-80) REVERT: A 166 GLU cc_start: 0.7645 (tp30) cc_final: 0.6871 (tt0) REVERT: A 193 MET cc_start: 0.3698 (mtt) cc_final: 0.3180 (mmm) REVERT: A 307 LYS cc_start: 0.7847 (tmtt) cc_final: 0.7375 (mmtt) REVERT: A 368 TRP cc_start: 0.5037 (m-10) cc_final: 0.4826 (m-10) REVERT: A 369 TRP cc_start: 0.4624 (m100) cc_final: 0.4412 (m-10) REVERT: B 12 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8509 (pt) REVERT: B 324 LYS cc_start: 0.7938 (tmtt) cc_final: 0.6984 (mttp) REVERT: C 219 TRP cc_start: 0.7347 (t60) cc_final: 0.6976 (t60) REVERT: C 286 GLU cc_start: 0.7295 (pt0) cc_final: 0.6900 (pm20) REVERT: C 295 LEU cc_start: 0.8123 (pt) cc_final: 0.7659 (tp) REVERT: C 411 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7576 (ttpp) REVERT: D 117 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8630 (mm) REVERT: D 303 MET cc_start: 0.8756 (tmm) cc_final: 0.8334 (tmm) REVERT: D 430 GLN cc_start: 0.9016 (tp40) cc_final: 0.8484 (mm-40) REVERT: D 497 LYS cc_start: 0.8431 (mptt) cc_final: 0.8013 (mmtp) REVERT: E 3 ASN cc_start: 0.8581 (p0) cc_final: 0.8210 (p0) REVERT: E 136 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: E 156 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: E 193 MET cc_start: 0.5389 (tpp) cc_final: 0.5161 (tpp) REVERT: E 208 VAL cc_start: 0.7491 (t) cc_final: 0.7182 (p) REVERT: E 395 MET cc_start: 0.5725 (mmm) cc_final: 0.4771 (mmm) REVERT: F 29 LEU cc_start: 0.9009 (tp) cc_final: 0.8611 (mt) REVERT: F 79 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: F 303 MET cc_start: 0.8005 (ttm) cc_final: 0.7771 (ttt) REVERT: G 193 MET cc_start: 0.2658 (ptp) cc_final: 0.2000 (ptp) REVERT: G 285 TYR cc_start: 0.6703 (t80) cc_final: 0.6231 (t80) REVERT: H 62 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8075 (ptmm) REVERT: H 317 VAL cc_start: 0.8921 (t) cc_final: 0.8695 (t) REVERT: H 352 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: H 411 TYR cc_start: 0.8163 (t80) cc_final: 0.7248 (t80) REVERT: H 429 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6798 (tp) outliers start: 60 outliers final: 49 residues processed: 303 average time/residue: 0.1661 time to fit residues: 84.8244 Evaluate side-chains 305 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 192 TRP Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 352 GLU Chi-restraints excluded: chain H residue 403 TYR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 66 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 348 optimal weight: 0.0470 chunk 354 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 258 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS B 468 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107871 restraints weight = 66077.266| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.65 r_work: 0.3514 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 33160 Z= 0.180 Angle : 0.690 59.149 45402 Z= 0.384 Chirality : 0.043 0.570 4984 Planarity : 0.005 0.078 5242 Dihedral : 18.318 179.023 5970 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 1.97 % Allowed : 15.36 % Favored : 82.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3532 helix: 1.08 (0.15), residues: 1214 sheet: -1.13 (0.22), residues: 592 loop : -1.33 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 225 TYR 0.024 0.001 TYR G 293 PHE 0.030 0.001 PHE G 343 TRP 0.018 0.001 TRP F 370 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00379 (33160) covalent geometry : angle 0.69003 (45402) hydrogen bonds : bond 0.04046 ( 1092) hydrogen bonds : angle 5.08283 ( 2950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7537.14 seconds wall clock time: 130 minutes 19.69 seconds (7819.69 seconds total)