Starting phenix.real_space_refine on Fri May 30 04:28:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozi_17310/05_2025/8ozi_17310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozi_17310/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozi_17310/05_2025/8ozi_17310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozi_17310/05_2025/8ozi_17310.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozi_17310/05_2025/8ozi_17310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozi_17310/05_2025/8ozi_17310.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.79, per 1000 atoms: 0.55 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: 9.79 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 11.77 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: 12.70 Time building geometry restraints manager: 11.08 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: 0.00 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 80.250 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.210 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.042 0.002 TRP F 370 HIS 0.006 0.001 HIS C 160 PHE 0.026 0.002 PHE A 332 TYR 0.018 0.001 TYR G 285 ARG 0.007 0.001 ARG F 225 Details of bonding type rmsd hydrogen bonds : bond 0.20974 ( 1092) hydrogen bonds : angle 8.20964 ( 2950) covalent geometry : bond 0.00535 (33160) covalent geometry : angle 0.77102 (45402) *********************** 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 : 3.763 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: 0.3965 time to fit residues: 243.0047 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 : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 20.0000 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 0.0980 chunk 109 optimal weight: 0.0270 chunk 171 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 326 optimal weight: 0.8980 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 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 370 ASN F 61 GLN F 302 GLN H 251 HIS H 430 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.140643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110432 restraints weight = 65522.115| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.76 r_work: 0.3534 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33160 Z= 0.127 Angle : 0.597 9.387 45402 Z= 0.315 Chirality : 0.042 0.232 4984 Planarity : 0.005 0.062 5242 Dihedral : 18.462 179.890 5970 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.64 % Favored : 94.93 % Rotamer: Outliers : 0.84 % Allowed : 6.73 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3532 helix: 0.66 (0.15), residues: 1218 sheet: -0.86 (0.21), residues: 610 loop : -1.12 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 219 HIS 0.005 0.001 HIS A 160 PHE 0.022 0.002 PHE A 343 TYR 0.023 0.001 TYR C 233 ARG 0.005 0.001 ARG F 225 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 1092) hydrogen bonds : angle 5.76286 ( 2950) covalent geometry : bond 0.00277 (33160) covalent geometry : angle 0.59654 (45402) *********************** 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 337 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 310 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.3761 (mtt) cc_final: 0.3257 (mmm) REVERT: B 122 ILE cc_start: 0.8870 (tt) cc_final: 0.8652 (tt) REVERT: C 295 LEU cc_start: 0.7753 (pt) cc_final: 0.7460 (tp) REVERT: D 430 GLN cc_start: 0.8633 (tp40) cc_final: 0.8231 (mm-40) REVERT: E 3 ASN cc_start: 0.8564 (p0) cc_final: 0.8248 (p0) REVERT: E 257 ARG cc_start: 0.5627 (mmm-85) cc_final: 0.5400 (mmm-85) REVERT: F 303 MET cc_start: 0.8007 (ttm) cc_final: 0.7752 (ttt) REVERT: F 474 ASP cc_start: 0.7689 (t0) cc_final: 0.7450 (t0) REVERT: G 395 MET cc_start: 0.6655 (mmt) cc_final: 0.6404 (mmt) REVERT: H 101 ILE cc_start: 0.8753 (tt) cc_final: 0.8540 (tp) REVERT: H 387 THR cc_start: 0.8973 (t) cc_final: 0.8757 (m) REVERT: H 435 MET cc_start: 0.4946 (mmt) cc_final: 0.4629 (mmt) outliers start: 27 outliers final: 20 residues processed: 321 average time/residue: 0.4049 time to fit residues: 215.6014 Evaluate side-chains 273 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 253 time to evaluate : 3.267 ------------------------------------------------------------------------------- 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 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 318 ASN Chi-restraints excluded: chain E residue 370 ASN 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 74 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 109 ASN B 59 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN F 367 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.140355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110020 restraints weight = 65931.685| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.76 r_work: 0.3532 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33160 Z= 0.123 Angle : 0.556 8.735 45402 Z= 0.294 Chirality : 0.042 0.223 4984 Planarity : 0.005 0.058 5242 Dihedral : 18.427 178.904 5970 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.61 % Favored : 94.99 % Rotamer: Outliers : 1.28 % Allowed : 8.89 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3532 helix: 0.75 (0.15), residues: 1242 sheet: -0.80 (0.21), residues: 606 loop : -1.13 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 219 HIS 0.006 0.001 HIS G 320 PHE 0.017 0.001 PHE A 332 TYR 0.017 0.001 TYR G 293 ARG 0.003 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1092) hydrogen bonds : angle 5.34504 ( 2950) covalent geometry : bond 0.00275 (33160) covalent geometry : angle 0.55623 (45402) *********************** 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 340 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 299 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TYR cc_start: 0.8503 (m-80) cc_final: 0.8277 (m-80) REVERT: A 193 MET cc_start: 0.3820 (mtt) cc_final: 0.3276 (mmm) REVERT: B 1 MET cc_start: 0.4773 (mmp) cc_final: 0.4555 (mmp) REVERT: B 40 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7780 (mtmt) REVERT: B 68 ASN cc_start: 0.7815 (t0) cc_final: 0.7034 (m-40) REVERT: B 122 ILE cc_start: 0.8880 (tt) cc_final: 0.8655 (tt) REVERT: B 324 LYS cc_start: 0.7967 (tmtt) cc_final: 0.6904 (mtmm) REVERT: B 435 MET cc_start: 0.6520 (mmm) cc_final: 0.6303 (mmt) REVERT: C 126 ARG cc_start: 0.6886 (mmp-170) cc_final: 0.6013 (tpp80) REVERT: C 162 LYS cc_start: 0.4508 (mmpt) cc_final: 0.4071 (mmpt) REVERT: C 219 TRP cc_start: 0.7132 (t60) cc_final: 0.6919 (t60) REVERT: C 295 LEU cc_start: 0.7781 (pt) cc_final: 0.7485 (tp) REVERT: C 371 ASN cc_start: 0.8172 (m-40) cc_final: 0.7696 (t0) REVERT: D 430 GLN cc_start: 0.8683 (tp40) cc_final: 0.8139 (mm-40) REVERT: E 3 ASN cc_start: 0.8541 (p0) cc_final: 0.8194 (p0) REVERT: E 257 ARG cc_start: 0.5582 (mmm-85) cc_final: 0.5291 (mmm-85) REVERT: F 303 MET cc_start: 0.8049 (ttm) cc_final: 0.7823 (ttt) REVERT: F 435 MET cc_start: 0.6955 (mmp) cc_final: 0.6730 (mmt) REVERT: G 193 MET cc_start: 0.3837 (mtt) cc_final: 0.3591 (mtm) REVERT: G 373 TRP cc_start: 0.7906 (m100) cc_final: 0.7504 (m100) REVERT: H 62 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7937 (ptmm) REVERT: H 248 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.8008 (mp) REVERT: H 356 GLU cc_start: 0.7848 (tp30) cc_final: 0.7633 (tt0) outliers start: 41 outliers final: 27 residues processed: 320 average time/residue: 0.4112 time to fit residues: 217.9147 Evaluate side-chains 284 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 3.680 ------------------------------------------------------------------------------- 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 C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 145 ASP 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 E residue 279 ASP Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 366 LYS Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 203 ASP 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 248 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 317 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 292 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** B 439 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS D 135 ASN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 HIS H 368 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.136639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106283 restraints weight = 65832.100| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.73 r_work: 0.3474 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33160 Z= 0.183 Angle : 0.599 8.788 45402 Z= 0.313 Chirality : 0.043 0.253 4984 Planarity : 0.005 0.062 5242 Dihedral : 18.456 179.972 5970 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.07 % Favored : 94.54 % Rotamer: Outliers : 2.03 % Allowed : 10.26 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3532 helix: 0.78 (0.15), residues: 1232 sheet: -0.85 (0.22), residues: 590 loop : -1.17 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 219 HIS 0.006 0.001 HIS D 251 PHE 0.033 0.002 PHE A 223 TYR 0.021 0.001 TYR A 416 ARG 0.004 0.001 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1092) hydrogen bonds : angle 5.28227 ( 2950) covalent geometry : bond 0.00424 (33160) covalent geometry : angle 0.59922 (45402) *********************** 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 347 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 282 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TYR cc_start: 0.8672 (m-80) cc_final: 0.8450 (m-80) REVERT: A 193 MET cc_start: 0.3693 (mtt) cc_final: 0.3139 (mmm) REVERT: A 277 MET cc_start: 0.7166 (mmm) cc_final: 0.6751 (mmm) REVERT: B 1 MET cc_start: 0.4744 (mmp) cc_final: 0.4539 (mmp) REVERT: B 324 LYS cc_start: 0.7825 (tmtt) cc_final: 0.6745 (mtmm) REVERT: C 219 TRP cc_start: 0.7151 (t60) cc_final: 0.6915 (t60) REVERT: C 295 LEU cc_start: 0.7879 (pt) cc_final: 0.7528 (tp) REVERT: C 371 ASN cc_start: 0.8197 (m-40) cc_final: 0.7723 (t0) REVERT: D 150 TYR cc_start: 0.7905 (m-80) cc_final: 0.7532 (m-80) REVERT: D 430 GLN cc_start: 0.8807 (tp40) cc_final: 0.8242 (mm-40) REVERT: E 3 ASN cc_start: 0.8639 (p0) cc_final: 0.8252 (p0) REVERT: E 136 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: F 30 PHE cc_start: 0.8270 (m-80) cc_final: 0.7787 (m-80) REVERT: F 79 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: F 100 ASP cc_start: 0.7846 (m-30) cc_final: 0.7576 (m-30) REVERT: F 303 MET cc_start: 0.8131 (ttm) cc_final: 0.7888 (ttt) REVERT: G 193 MET cc_start: 0.4018 (mtt) cc_final: 0.3805 (mtm) REVERT: G 373 TRP cc_start: 0.7909 (m100) cc_final: 0.7518 (m100) REVERT: H 62 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8015 (ptmm) REVERT: H 248 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8076 (mp) outliers start: 65 outliers final: 45 residues processed: 319 average time/residue: 0.3910 time to fit residues: 209.7535 Evaluate side-chains 301 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR 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 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 C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN 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 136 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 289 ASN 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 229 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 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 387 THR 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 280 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 259 optimal weight: 0.4980 chunk 323 optimal weight: 0.7980 chunk 106 optimal weight: 0.0470 chunk 124 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 203 optimal weight: 0.4980 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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** B 468 ASN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.139564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109406 restraints weight = 65449.735| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.75 r_work: 0.3524 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33160 Z= 0.109 Angle : 0.543 9.420 45402 Z= 0.285 Chirality : 0.041 0.223 4984 Planarity : 0.004 0.063 5242 Dihedral : 18.332 179.805 5970 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.59 % Favored : 95.07 % Rotamer: Outliers : 1.50 % Allowed : 11.58 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3532 helix: 0.92 (0.15), residues: 1238 sheet: -0.66 (0.22), residues: 570 loop : -1.15 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 219 HIS 0.005 0.001 HIS G 320 PHE 0.019 0.001 PHE F 30 TYR 0.020 0.001 TYR G 293 ARG 0.003 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 1092) hydrogen bonds : angle 5.09168 ( 2950) covalent geometry : bond 0.00242 (33160) covalent geometry : angle 0.54349 (45402) *********************** 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 335 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6533 (m100) cc_final: 0.5556 (m100) REVERT: A 193 MET cc_start: 0.3764 (mtt) cc_final: 0.3227 (mmm) REVERT: A 277 MET cc_start: 0.7107 (mmm) cc_final: 0.6715 (mmm) REVERT: B 1 MET cc_start: 0.4563 (mmp) cc_final: 0.4361 (mmp) REVERT: B 12 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8535 (pt) REVERT: B 68 ASN cc_start: 0.7941 (t0) cc_final: 0.6935 (m-40) REVERT: B 324 LYS cc_start: 0.7813 (tmtt) cc_final: 0.6825 (mtmm) REVERT: C 219 TRP cc_start: 0.7213 (t60) cc_final: 0.6762 (t60) REVERT: C 286 GLU cc_start: 0.7437 (pt0) cc_final: 0.7123 (pm20) REVERT: C 295 LEU cc_start: 0.7863 (pt) cc_final: 0.7559 (tp) REVERT: C 371 ASN cc_start: 0.8167 (m-40) cc_final: 0.7704 (t0) REVERT: C 411 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7622 (ttpp) REVERT: D 150 TYR cc_start: 0.7947 (m-80) cc_final: 0.7617 (m-80) REVERT: D 430 GLN cc_start: 0.8781 (tp40) cc_final: 0.8133 (mm-40) REVERT: E 3 ASN cc_start: 0.8537 (p0) cc_final: 0.8164 (p0) REVERT: E 136 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: F 29 LEU cc_start: 0.9174 (tp) cc_final: 0.8802 (mt) REVERT: F 79 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: F 100 ASP cc_start: 0.7829 (m-30) cc_final: 0.7522 (m-30) REVERT: F 303 MET cc_start: 0.8112 (ttm) cc_final: 0.7907 (ttt) REVERT: G 158 PHE cc_start: 0.6731 (t80) cc_final: 0.5910 (t80) REVERT: H 62 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7978 (ptmm) outliers start: 48 outliers final: 34 residues processed: 317 average time/residue: 0.4101 time to fit residues: 217.1900 Evaluate side-chains 298 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 3.537 ------------------------------------------------------------------------------- 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 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 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 D residue 248 ILE Chi-restraints excluded: chain D residue 303 MET 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 194 LEU 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 229 LEU 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 247 LEU Chi-restraints excluded: chain H residue 105 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 136 optimal weight: 1.9990 chunk 339 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 248 optimal weight: 0.2980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4078 r_free = 0.4078 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108208 restraints weight = 65993.802| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.74 r_work: 0.3506 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33160 Z= 0.131 Angle : 0.548 9.654 45402 Z= 0.286 Chirality : 0.041 0.224 4984 Planarity : 0.004 0.065 5242 Dihedral : 18.293 179.581 5970 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.10 % Favored : 94.65 % Rotamer: Outliers : 1.78 % Allowed : 12.17 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3532 helix: 1.02 (0.15), residues: 1230 sheet: -0.76 (0.22), residues: 592 loop : -1.13 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 219 HIS 0.005 0.001 HIS G 320 PHE 0.023 0.001 PHE G 343 TYR 0.016 0.001 TYR G 293 ARG 0.003 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 1092) hydrogen bonds : angle 5.04553 ( 2950) covalent geometry : bond 0.00300 (33160) covalent geometry : angle 0.54760 (45402) *********************** 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 345 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6643 (m100) cc_final: 0.5643 (m100) REVERT: A 193 MET cc_start: 0.3819 (mtt) cc_final: 0.3285 (mmm) REVERT: B 12 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8519 (pt) REVERT: B 68 ASN cc_start: 0.7972 (t0) cc_final: 0.6924 (m-40) REVERT: B 324 LYS cc_start: 0.7778 (tmtt) cc_final: 0.6754 (mtmm) REVERT: C 219 TRP cc_start: 0.7226 (t60) cc_final: 0.6809 (t60) REVERT: C 286 GLU cc_start: 0.7413 (pt0) cc_final: 0.7092 (pm20) REVERT: C 295 LEU cc_start: 0.7889 (pt) cc_final: 0.7578 (tp) REVERT: C 371 ASN cc_start: 0.8113 (m-40) cc_final: 0.7787 (t0) REVERT: C 411 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7551 (ttpp) REVERT: D 117 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 150 TYR cc_start: 0.7955 (m-80) cc_final: 0.7667 (m-80) REVERT: D 430 GLN cc_start: 0.8775 (tp40) cc_final: 0.8065 (mm-40) REVERT: E 3 ASN cc_start: 0.8564 (p0) cc_final: 0.8174 (p0) REVERT: E 136 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: F 29 LEU cc_start: 0.9224 (tp) cc_final: 0.8817 (mt) REVERT: F 79 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: F 303 MET cc_start: 0.8235 (ttm) cc_final: 0.7969 (ttt) REVERT: G 158 PHE cc_start: 0.6837 (t80) cc_final: 0.6039 (t80) REVERT: G 373 TRP cc_start: 0.8015 (m100) cc_final: 0.7543 (m100) REVERT: H 62 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8000 (ptmm) outliers start: 57 outliers final: 43 residues processed: 324 average time/residue: 0.3834 time to fit residues: 206.9019 Evaluate side-chains 308 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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 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 344 GLN 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 194 LEU Chi-restraints excluded: chain E residue 247 LEU 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 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 405 ILE Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 429 ILE 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 273 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 205 GLN B 207 HIS B 468 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.136356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.106200 restraints weight = 65797.569| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.72 r_work: 0.3474 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 33160 Z= 0.169 Angle : 0.581 10.442 45402 Z= 0.303 Chirality : 0.042 0.229 4984 Planarity : 0.005 0.070 5242 Dihedral : 18.308 179.669 5970 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 2.00 % Allowed : 12.77 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3532 helix: 1.01 (0.15), residues: 1240 sheet: -0.87 (0.22), residues: 596 loop : -1.23 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 219 HIS 0.005 0.001 HIS D 251 PHE 0.031 0.002 PHE G 343 TYR 0.035 0.001 TYR A 251 ARG 0.006 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 1092) hydrogen bonds : angle 5.09716 ( 2950) covalent geometry : bond 0.00391 (33160) covalent geometry : angle 0.58061 (45402) *********************** 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 339 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6686 (m100) cc_final: 0.5630 (m100) REVERT: A 193 MET cc_start: 0.3736 (mtt) cc_final: 0.3193 (mmm) REVERT: B 12 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8506 (pt) REVERT: B 324 LYS cc_start: 0.7833 (tmtt) cc_final: 0.6775 (mtmm) REVERT: C 219 TRP cc_start: 0.7245 (t60) cc_final: 0.6837 (t60) REVERT: C 286 GLU cc_start: 0.7407 (pt0) cc_final: 0.7064 (pm20) REVERT: C 295 LEU cc_start: 0.7939 (pt) cc_final: 0.7608 (tp) REVERT: C 371 ASN cc_start: 0.8101 (m-40) cc_final: 0.7838 (t0) REVERT: D 117 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8558 (mm) REVERT: D 430 GLN cc_start: 0.8883 (tp40) cc_final: 0.8061 (mm-40) REVERT: D 497 LYS cc_start: 0.8438 (mptt) cc_final: 0.7995 (mmtp) REVERT: E 3 ASN cc_start: 0.8646 (p0) cc_final: 0.8250 (p0) REVERT: E 136 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: E 156 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: F 29 LEU cc_start: 0.9187 (tp) cc_final: 0.8769 (mt) REVERT: F 79 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: F 303 MET cc_start: 0.8166 (ttm) cc_final: 0.7931 (ttt) REVERT: F 325 ASN cc_start: 0.8753 (t0) cc_final: 0.8496 (t0) REVERT: F 435 MET cc_start: 0.6603 (mmt) cc_final: 0.6223 (mmt) REVERT: G 158 PHE cc_start: 0.6808 (t80) cc_final: 0.6099 (t80) REVERT: H 62 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7992 (ptmm) outliers start: 64 outliers final: 49 residues processed: 317 average time/residue: 0.3999 time to fit residues: 213.0147 Evaluate side-chains 304 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 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 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 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 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 344 GLN 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 75 LEU 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 194 LEU Chi-restraints excluded: chain E residue 247 LEU 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 89 THR 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 302 GLN 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 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 83 ASP Chi-restraints excluded: chain H residue 105 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 Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 25 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 294 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 302 GLN ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.136350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.106494 restraints weight = 66343.861| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.66 r_work: 0.3487 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33160 Z= 0.213 Angle : 0.625 11.143 45402 Z= 0.325 Chirality : 0.044 0.237 4984 Planarity : 0.005 0.075 5242 Dihedral : 18.393 179.681 5970 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.78 % Favored : 93.97 % Rotamer: Outliers : 2.28 % Allowed : 13.33 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3532 helix: 0.92 (0.15), residues: 1228 sheet: -1.05 (0.22), residues: 600 loop : -1.33 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 219 HIS 0.005 0.001 HIS G 320 PHE 0.024 0.002 PHE A 332 TYR 0.025 0.002 TYR A 251 ARG 0.007 0.001 ARG H 243 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 1092) hydrogen bonds : angle 5.22046 ( 2950) covalent geometry : bond 0.00494 (33160) covalent geometry : angle 0.62515 (45402) *********************** 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: 73 poor density : 265 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6727 (m100) cc_final: 0.5564 (m100) REVERT: A 193 MET cc_start: 0.3725 (mtt) cc_final: 0.3177 (mmm) REVERT: A 277 MET cc_start: 0.6954 (tpp) cc_final: 0.6750 (mmm) REVERT: B 12 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8558 (pt) REVERT: B 324 LYS cc_start: 0.7916 (tmtt) cc_final: 0.6782 (mtmm) REVERT: C 219 TRP cc_start: 0.7311 (t60) cc_final: 0.6922 (t60) REVERT: C 286 GLU cc_start: 0.7340 (pt0) cc_final: 0.7008 (pm20) REVERT: C 295 LEU cc_start: 0.8031 (pt) cc_final: 0.7649 (tp) REVERT: C 297 LYS cc_start: 0.6404 (mtpt) cc_final: 0.5812 (mtpt) REVERT: D 117 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8623 (mm) REVERT: D 150 TYR cc_start: 0.8025 (m-80) cc_final: 0.7714 (m-10) REVERT: D 430 GLN cc_start: 0.8911 (tp40) cc_final: 0.8639 (tp40) REVERT: E 3 ASN cc_start: 0.8591 (p0) cc_final: 0.8190 (p0) REVERT: E 136 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: E 156 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: E 394 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5739 (mt-10) REVERT: E 395 MET cc_start: 0.5965 (mmm) cc_final: 0.5378 (mmm) REVERT: F 79 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: F 303 MET cc_start: 0.8008 (ttm) cc_final: 0.7793 (ttt) REVERT: G 158 PHE cc_start: 0.6950 (t80) cc_final: 0.6386 (t80) REVERT: H 62 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8035 (ptmm) REVERT: H 352 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7962 (tp30) outliers start: 73 outliers final: 53 residues processed: 313 average time/residue: 0.4085 time to fit residues: 213.3088 Evaluate side-chains 305 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 3.664 ------------------------------------------------------------------------------- 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 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 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 162 LYS 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 303 MET 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 437 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 75 LEU 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 194 LEU Chi-restraints excluded: chain E residue 247 LEU 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 89 THR 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 302 GLN 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 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 83 ASP Chi-restraints excluded: chain H residue 105 LEU 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 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 296 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 256 optimal weight: 0.0870 chunk 226 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 267 optimal weight: 0.0070 chunk 30 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 337 optimal weight: 8.9990 chunk 227 optimal weight: 0.0770 overall best weight: 1.0336 ------------------------------------------------------------------------------- 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 ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.138953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.109266 restraints weight = 66342.977| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.66 r_work: 0.3534 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33160 Z= 0.126 Angle : 0.567 10.740 45402 Z= 0.297 Chirality : 0.042 0.226 4984 Planarity : 0.004 0.075 5242 Dihedral : 18.288 178.188 5970 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.84 % Favored : 94.96 % Rotamer: Outliers : 1.78 % Allowed : 14.46 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3532 helix: 1.04 (0.15), residues: 1244 sheet: -0.97 (0.22), residues: 596 loop : -1.27 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 219 HIS 0.004 0.001 HIS G 188 PHE 0.023 0.001 PHE A 332 TYR 0.024 0.001 TYR A 251 ARG 0.003 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 1092) hydrogen bonds : angle 5.06374 ( 2950) covalent geometry : bond 0.00286 (33160) covalent geometry : angle 0.56675 (45402) *********************** 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 326 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.3726 (mtt) cc_final: 0.3203 (mmm) REVERT: A 395 MET cc_start: 0.2772 (ptm) cc_final: 0.2444 (ptm) REVERT: B 324 LYS cc_start: 0.7766 (tmtt) cc_final: 0.6841 (mttp) REVERT: C 219 TRP cc_start: 0.7334 (t60) cc_final: 0.6939 (t60) REVERT: C 295 LEU cc_start: 0.8018 (pt) cc_final: 0.7679 (tp) REVERT: D 117 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8596 (mm) REVERT: D 150 TYR cc_start: 0.7988 (m-80) cc_final: 0.7685 (m-10) REVERT: D 430 GLN cc_start: 0.8946 (tp40) cc_final: 0.8119 (mm-40) REVERT: D 497 LYS cc_start: 0.8433 (mptt) cc_final: 0.8022 (mmtp) REVERT: E 3 ASN cc_start: 0.8527 (p0) cc_final: 0.8158 (p0) REVERT: E 136 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: E 156 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: E 394 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5871 (mt-10) REVERT: E 395 MET cc_start: 0.6055 (mmm) cc_final: 0.5547 (mmm) REVERT: E 417 ASN cc_start: 0.7024 (p0) cc_final: 0.6768 (p0) REVERT: F 29 LEU cc_start: 0.9114 (tp) cc_final: 0.8714 (mt) REVERT: F 79 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: F 209 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: G 158 PHE cc_start: 0.6985 (t80) cc_final: 0.6399 (t80) REVERT: G 285 TYR cc_start: 0.6736 (t80) cc_final: 0.6290 (t80) REVERT: G 383 TYR cc_start: 0.5465 (t80) cc_final: 0.5168 (t80) REVERT: H 62 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8012 (ptmm) REVERT: H 352 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7971 (tp30) outliers start: 57 outliers final: 43 residues processed: 306 average time/residue: 0.3884 time to fit residues: 198.9908 Evaluate side-chains 299 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 372 THR 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 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 162 LYS 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 344 GLN 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 75 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 247 LEU 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 209 GLN 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 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 105 LEU 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 437 VAL 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 348 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 168 optimal weight: 0.0270 chunk 146 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 161 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 overall best weight: 1.3620 ------------------------------------------------------------------------------- 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 ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 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 = 0.4093 r_free = 0.4093 target = 0.138626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.108914 restraints weight = 66133.702| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.66 r_work: 0.3530 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33160 Z= 0.139 Angle : 0.574 9.561 45402 Z= 0.298 Chirality : 0.042 0.224 4984 Planarity : 0.004 0.075 5242 Dihedral : 18.268 178.142 5970 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.27 % Favored : 94.54 % Rotamer: Outliers : 1.72 % Allowed : 14.67 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3532 helix: 1.08 (0.15), residues: 1244 sheet: -0.91 (0.23), residues: 574 loop : -1.28 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 219 HIS 0.005 0.001 HIS G 320 PHE 0.023 0.001 PHE A 332 TYR 0.024 0.001 TYR G 293 ARG 0.003 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1092) hydrogen bonds : angle 5.05455 ( 2950) covalent geometry : bond 0.00319 (33160) covalent geometry : angle 0.57423 (45402) ********************** 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 311 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.3666 (mtt) cc_final: 0.3144 (mmm) REVERT: A 395 MET cc_start: 0.2641 (ptm) cc_final: 0.2240 (ptm) REVERT: B 324 LYS cc_start: 0.7758 (tmtt) cc_final: 0.6853 (mttp) REVERT: C 143 GLU cc_start: 0.7443 (tp30) cc_final: 0.7241 (tp30) REVERT: C 219 TRP cc_start: 0.7276 (t60) cc_final: 0.6922 (t60) REVERT: C 286 GLU cc_start: 0.7333 (pt0) cc_final: 0.7031 (pm20) REVERT: C 295 LEU cc_start: 0.8009 (pt) cc_final: 0.7660 (tp) REVERT: C 411 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7583 (ttpp) REVERT: D 117 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8618 (mm) REVERT: D 150 TYR cc_start: 0.7992 (m-80) cc_final: 0.7687 (m-10) REVERT: D 430 GLN cc_start: 0.8953 (tp40) cc_final: 0.8206 (mm-40) REVERT: D 497 LYS cc_start: 0.8440 (mptt) cc_final: 0.8029 (mmtp) REVERT: E 3 ASN cc_start: 0.8591 (p0) cc_final: 0.8221 (p0) REVERT: E 136 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7295 (pm20) REVERT: E 156 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: E 417 ASN cc_start: 0.6928 (p0) cc_final: 0.6694 (p0) REVERT: F 79 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: F 209 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: G 158 PHE cc_start: 0.6959 (t80) cc_final: 0.6350 (t80) REVERT: G 193 MET cc_start: 0.2573 (ptp) cc_final: 0.1874 (ptp) REVERT: G 285 TYR cc_start: 0.6729 (t80) cc_final: 0.6252 (t80) REVERT: G 300 LEU cc_start: 0.6981 (mt) cc_final: 0.6678 (tp) REVERT: H 62 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8027 (ptmm) REVERT: H 352 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7970 (tp30) outliers start: 55 outliers final: 46 residues processed: 291 average time/residue: 0.4033 time to fit residues: 195.4093 Evaluate side-chains 296 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 372 THR 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 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 162 LYS 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 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 40 ASP Chi-restraints excluded: chain E residue 75 LEU 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 194 LEU Chi-restraints excluded: chain E residue 247 LEU 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 209 GLN 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 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 105 LEU 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 437 VAL 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 278 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 337 optimal weight: 7.9990 chunk 311 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.139471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109852 restraints weight = 66048.087| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.67 r_work: 0.3545 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33160 Z= 0.122 Angle : 0.558 8.959 45402 Z= 0.291 Chirality : 0.041 0.221 4984 Planarity : 0.004 0.073 5242 Dihedral : 18.219 177.386 5970 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.76 % Rotamer: Outliers : 1.81 % Allowed : 14.77 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3532 helix: 1.13 (0.15), residues: 1244 sheet: -0.87 (0.23), residues: 574 loop : -1.25 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 370 HIS 0.009 0.001 HIS G 320 PHE 0.023 0.001 PHE A 332 TYR 0.026 0.001 TYR G 293 ARG 0.003 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1092) hydrogen bonds : angle 5.01312 ( 2950) covalent geometry : bond 0.00278 (33160) covalent geometry : angle 0.55845 (45402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15712.56 seconds wall clock time: 273 minutes 9.63 seconds (16389.63 seconds total)