Starting phenix.real_space_refine on Mon Jul 6 05:33:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozg_17308/07_2026/8ozg_17308.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 6 Type Number sf(0) Gaussians P 136 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 20266 2.51 5 N 5310 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 136 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32077 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: "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: "E" 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: "F" 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: "G" 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: "H" 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: "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: "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: "M" 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: "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: 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: "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: "Q" 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'AR6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.03, per 1000 atoms: 0.22 Number of scatterers: 32077 At special positions: 0 Unit cell: (177.87, 208.12, 166.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 136 15.00 Mg 1 11.99 O 6268 8.00 N 5310 7.00 C 20266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 133 helices and 26 sheets defined 40.0% alpha, 14.9% beta 21 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.998A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 removed outlier: 3.676A 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 104 through 108 removed outlier: 4.160A pdb=" N ILE A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.767A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.077A 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 199 through 203 removed outlier: 3.860A pdb=" N GLU A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.750A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.649A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 4.021A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (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: 3.980A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.799A 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 23 through 31 Processing helix chain 'B' and resid 46 through 62 removed outlier: 4.012A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.604A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.639A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.616A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.533A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.777A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.583A pdb=" N TYR B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.524A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.508A pdb=" N ILE B 429 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.779A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.746A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.607A pdb=" N TYR B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 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 115 removed outlier: 3.770A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 139 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 removed outlier: 3.852A pdb=" N GLU C 202 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.224A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.604A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 265 through 280 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: 3.883A pdb=" N THR C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 23 through 31 Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.618A pdb=" N LYS E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.637A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.673A pdb=" N LYS E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.766A pdb=" N TYR E 148 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.561A pdb=" N VAL E 162 " --> pdb=" O LYS E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 214 removed outlier: 3.686A pdb=" N LEU E 214 " --> pdb=" O PHE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 Processing helix chain 'E' and resid 230 through 234 removed outlier: 3.785A pdb=" N ASP E 233 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 331 through 351 removed outlier: 3.993A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.934A pdb=" N TRP E 370 " --> pdb=" O ASN E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.865A pdb=" N SER E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 491 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.595A pdb=" N TYR E 505 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.827A pdb=" N ILE F 108 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 146 through 157 removed outlier: 4.025A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 219 through 224 removed outlier: 4.429A pdb=" N PHE F 223 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR F 224 " --> pdb=" O TYR F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 233 removed outlier: 4.055A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.565A pdb=" N LYS F 237 " --> pdb=" O HIS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 257 through 280 removed outlier: 4.163A pdb=" N ILE F 265 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 267 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 353 through 366 Processing helix chain 'F' and resid 369 through 385 removed outlier: 3.789A pdb=" N THR F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 376 " --> pdb=" O THR F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 31 Processing helix chain 'G' and resid 46 through 62 removed outlier: 3.811A pdb=" N LYS G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.852A pdb=" N PHE G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 105 " --> pdb=" O ILE G 101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 131 removed outlier: 3.760A pdb=" N LYS G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 150 removed outlier: 3.794A pdb=" N TYR G 148 " --> pdb=" O PRO G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 214 removed outlier: 3.608A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 248 through 264 removed outlier: 3.666A pdb=" N ALA G 259 " --> pdb=" O THR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 351 removed outlier: 4.189A pdb=" N GLN G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 377 removed outlier: 3.649A pdb=" N VAL G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 430 Processing helix chain 'G' and resid 451 through 463 removed outlier: 3.798A pdb=" N LEU G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 491 removed outlier: 3.828A pdb=" N ASP G 484 " --> pdb=" O LEU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 removed outlier: 3.730A pdb=" N TYR G 505 " --> pdb=" O ALA G 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 28 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.605A pdb=" N GLN H 70 " --> pdb=" O TYR H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 71 through 89 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 123 through 139 removed outlier: 3.728A pdb=" N GLY H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 128 " --> pdb=" O TRP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.548A pdb=" N GLU H 202 " --> pdb=" O ASP H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 224 removed outlier: 4.290A pdb=" N PHE H 223 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 224 " --> pdb=" O TYR H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 233 removed outlier: 4.007A pdb=" N THR H 232 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 238 removed outlier: 3.616A pdb=" N THR H 238 " --> pdb=" O LYS H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 249 Processing helix chain 'H' and resid 257 through 280 removed outlier: 4.052A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 366 Processing helix chain 'H' and resid 369 through 384 removed outlier: 4.042A pdb=" N THR H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 376 " --> pdb=" O THR H 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 22 through 31 removed outlier: 3.636A pdb=" N GLY M 26 " --> pdb=" O ASP M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 62 removed outlier: 3.930A pdb=" N LYS M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE M 52 " --> pdb=" O GLN M 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 Processing helix chain 'M' and resid 97 through 106 removed outlier: 3.538A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 105 " --> pdb=" O ILE M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 132 removed outlier: 3.646A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 150 Processing helix chain 'M' and resid 158 through 162 removed outlier: 3.675A pdb=" N VAL M 162 " --> pdb=" O LYS M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 214 Processing helix chain 'M' and resid 215 through 218 Processing helix chain 'M' and resid 230 through 234 removed outlier: 3.509A pdb=" N ASP M 233 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 264 Processing helix chain 'M' and resid 331 through 351 removed outlier: 3.990A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 377 removed outlier: 3.553A pdb=" N ALA M 372 " --> pdb=" O GLN M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 430 Processing helix chain 'M' and resid 451 through 463 removed outlier: 3.815A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER M 461 " --> pdb=" O LYS M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 477 through 491 removed outlier: 3.711A pdb=" N ASP M 484 " --> pdb=" O LEU M 480 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 removed outlier: 3.657A pdb=" N TYR M 505 " --> pdb=" O ALA M 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.239A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.219A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 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: 4.222A pdb=" N ASN A 413 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR B 6 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 10.157A 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 removed outlier: 7.693A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 300 " --> pdb=" O GLU B 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 311 through 320 current: chain 'B' and resid 385 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 385 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 removed outlier: 3.505A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) 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 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.651A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS C 4 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU C 61 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE C 6 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 63 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER C 8 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 180 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: 3.993A pdb=" N ASN C 413 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR E 6 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N SER C 415 " --> pdb=" O TYR E 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 6 current: chain 'E' and resid 297 through 305 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 311 through 315 current: chain 'E' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 389 current: chain 'E' and resid 417 through 420 Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 305 removed outlier: 3.502A pdb=" N PHE C 305 " --> pdb=" O THR C 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB3, first strand: chain 'E' and resid 92 through 95 removed outlier: 7.026A pdb=" N SER E 41 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LYS E 94 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 43 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.646A pdb=" N VAL E 426 " --> pdb=" O THR E 431 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.134A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS F 4 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU F 61 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE F 6 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL F 63 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER F 8 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 62 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 165 through 172 removed outlier: 5.578A pdb=" N LYS F 167 " --> pdb=" O VAL F 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS G 2 " --> pdb=" O LYS F 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN F 413 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR G 6 " --> pdb=" O ASN F 413 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N SER F 415 " --> pdb=" O TYR G 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 6 current: chain 'G' and resid 297 through 305 removed outlier: 7.144A pdb=" N CYS G 298 " --> pdb=" O GLY G 318 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLY G 318 " --> pdb=" O CYS G 298 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G 300 " --> pdb=" O GLU G 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 311 through 320 current: chain 'G' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 382 through 389 current: chain 'G' and resid 417 through 420 Processing sheet with id=AB7, first strand: chain 'F' and resid 175 through 180 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 175 through 180 current: chain 'F' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 291 through 294 current: chain 'F' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 334 through 344 current: chain 'F' and resid 400 through 404 Processing sheet with id=AB8, first strand: chain 'F' and resid 208 through 210 Processing sheet with id=AB9, first strand: chain 'F' and resid 304 through 305 Processing sheet with id=AC1, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.669A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP G 139 " --> pdb=" O GLN G 222 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE G 224 " --> pdb=" O TRP G 139 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL G 141 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 32 through 33 removed outlier: 5.743A pdb=" N ILE H 5 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS H 4 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU H 61 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE H 6 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL H 63 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER H 8 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE H 118 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 165 through 180 current: chain 'H' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 291 through 294 current: chain 'H' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 334 through 344 current: chain 'H' and resid 400 through 415 removed outlier: 8.294A pdb=" N LEU M 4 " --> pdb=" O LYS H 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS H 411 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR M 6 " --> pdb=" O LYS H 411 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASN H 413 " --> pdb=" O TYR M 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 3 through 6 current: chain 'M' and resid 297 through 301 removed outlier: 7.682A pdb=" N CYS M 298 " --> pdb=" O GLY M 318 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLY M 318 " --> pdb=" O CYS M 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 315 through 321 current: chain 'M' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 389 current: chain 'M' and resid 417 through 420 Processing sheet with id=AC5, first strand: chain 'H' and resid 186 through 188 Processing sheet with id=AC6, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'M' and resid 92 through 95 removed outlier: 7.083A pdb=" N SER M 41 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS M 94 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL M 43 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N PHE M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL M 141 " --> pdb=" O PHE M 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 304 through 305 1013 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8229 1.33 - 1.45: 7218 1.45 - 1.57: 17270 1.57 - 1.70: 277 1.70 - 1.82: 148 Bond restraints: 33142 Sorted by residual: bond pdb=" C2' AR6 H 501 " pdb=" C3' AR6 H 501 " ideal model delta sigma weight residual 1.532 1.233 0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C2' AR6 C 501 " pdb=" C3' AR6 C 501 " ideal model delta sigma weight residual 1.532 1.237 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3D AR6 H 501 " pdb=" C4D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.255 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C3D AR6 C 501 " pdb=" C4D AR6 C 501 " ideal model delta sigma weight residual 1.529 1.258 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C1D AR6 H 501 " pdb=" C2D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.283 0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 33137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 45099 3.35 - 6.70: 249 6.70 - 10.05: 20 10.05 - 13.41: 4 13.41 - 16.76: 4 Bond angle restraints: 45376 Sorted by residual: angle pdb=" CA PRO G 32 " pdb=" N PRO G 32 " pdb=" CD PRO G 32 " ideal model delta sigma weight residual 112.00 102.49 9.51 1.40e+00 5.10e-01 4.62e+01 angle pdb=" C ALA H 145 " pdb=" CA ALA H 145 " pdb=" CB ALA H 145 " ideal model delta sigma weight residual 116.63 109.91 6.72 1.16e+00 7.43e-01 3.36e+01 angle pdb=" CA PRO G 144 " pdb=" N PRO G 144 " pdb=" CD PRO G 144 " ideal model delta sigma weight residual 112.00 103.90 8.10 1.40e+00 5.10e-01 3.34e+01 angle pdb=" N PRO G 144 " pdb=" CD PRO G 144 " pdb=" CG PRO G 144 " ideal model delta sigma weight residual 103.20 94.66 8.54 1.50e+00 4.44e-01 3.24e+01 angle pdb=" O3A AR6 C 501 " pdb=" PA AR6 C 501 " pdb=" O5' AR6 C 501 " ideal model delta sigma weight residual 93.19 109.95 -16.76 3.00e+00 1.11e-01 3.12e+01 ... (remaining 45371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 19020 33.71 - 67.42: 583 67.42 - 101.12: 40 101.12 - 134.83: 4 134.83 - 168.54: 13 Dihedral angle restraints: 19660 sinusoidal: 9152 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U I 7 " pdb=" C1' U I 7 " pdb=" N1 U I 7 " pdb=" C2 U I 7 " ideal model delta sinusoidal sigma weight residual -160.00 8.54 -168.54 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U O 9 " pdb=" C1' U O 9 " pdb=" N1 U O 9 " pdb=" C2 U O 9 " ideal model delta sinusoidal sigma weight residual 200.00 34.44 165.56 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U N 13 " pdb=" C1' U N 13 " pdb=" N1 U N 13 " pdb=" C2 U N 13 " ideal model delta sinusoidal sigma weight residual 200.00 46.73 153.27 1 1.50e+01 4.44e-03 8.08e+01 ... (remaining 19657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4762 0.096 - 0.191: 216 0.191 - 0.287: 3 0.287 - 0.383: 2 0.383 - 0.478: 1 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CB VAL H 113 " pdb=" CA VAL H 113 " pdb=" CG1 VAL H 113 " pdb=" CG2 VAL H 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C3' AR6 C 501 " pdb=" C2' AR6 C 501 " pdb=" C4' AR6 C 501 " pdb=" O3' AR6 C 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' AR6 H 501 " pdb=" C2' AR6 H 501 " pdb=" C4' AR6 H 501 " pdb=" O3' AR6 H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4981 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 332 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO F 333 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO F 333 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO F 333 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 31 " 0.094 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO G 32 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO G 32 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO G 32 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 318 " -0.043 5.00e-02 4.00e+02 6.65e-02 7.08e+00 pdb=" N PRO E 319 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.036 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1669 2.72 - 3.27: 32589 3.27 - 3.81: 55005 3.81 - 4.36: 68185 4.36 - 4.90: 111280 Nonbonded interactions: 268728 Sorted by model distance: nonbonded pdb=" O PHE G 373 " pdb=" OG1 THR G 377 " model vdw 2.177 3.040 nonbonded pdb=" OG SER M 493 " pdb=" OD1 ASP M 495 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR F 416 " pdb=" O THR G 404 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR F 221 " pdb=" O TYR F 233 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU M 436 " pdb=" O2' U O 6 " model vdw 2.204 3.040 ... (remaining 268723 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 'F' selection = (chain 'H' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.550 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.006 0.299 33142 Z= 0.325 Angle : 0.738 16.758 45376 Z= 0.433 Chirality : 0.043 0.478 4984 Planarity : 0.005 0.146 5238 Dihedral : 16.154 168.539 12868 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.15 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 0.06 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3532 helix: 0.68 (0.15), residues: 1210 sheet: -0.84 (0.21), residues: 578 loop : -1.27 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 240 TYR 0.016 0.001 TYR G 56 PHE 0.025 0.002 PHE C 343 TRP 0.032 0.002 TRP M 320 HIS 0.005 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.33 (33142) covalent geometry : angle 0.73762 / 0.43 (45376) hydrogen bonds : bond 0.18812 / 12.38 ( 1055) hydrogen bonds : angle 7.36024 / 5.15 ( 2877) *********************** 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 428 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 GLU cc_start: 0.7607 (tp30) cc_final: 0.7362 (tp30) REVERT: E 40 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8011 (mtmt) REVERT: E 104 PHE cc_start: 0.6174 (m-10) cc_final: 0.5793 (m-10) REVERT: E 484 ASP cc_start: 0.7989 (t70) cc_final: 0.7522 (t0) REVERT: F 192 TRP cc_start: 0.6056 (p-90) cc_final: 0.5583 (p-90) REVERT: F 317 LYS cc_start: 0.5364 (mttm) cc_final: 0.5137 (mtmm) REVERT: G 58 ASP cc_start: 0.7778 (m-30) cc_final: 0.6977 (p0) REVERT: G 107 ASN cc_start: 0.7008 (t0) cc_final: 0.6595 (t0) REVERT: H 193 MET cc_start: 0.6679 (ttm) cc_final: 0.6425 (mmm) REVERT: H 222 ASP cc_start: 0.5177 (m-30) cc_final: 0.4630 (m-30) REVERT: H 277 MET cc_start: 0.8233 (mmm) cc_final: 0.7955 (mmp) REVERT: M 245 PHE cc_start: 0.7238 (m-10) cc_final: 0.6958 (m-10) REVERT: M 406 LEU cc_start: 0.8975 (mm) cc_final: 0.8767 (mm) outliers start: 1 outliers final: 0 residues processed: 427 average time/residue: 0.1692 time to fit residues: 120.9187 Evaluate side-chains 284 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 329 HIS E 446 ASN F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN ** M 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.119634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.095953 restraints weight = 88333.436| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.32 r_work: 0.3550 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33142 Z= 0.177 Angle : 0.646 10.946 45376 Z= 0.341 Chirality : 0.044 0.288 4984 Planarity : 0.005 0.100 5238 Dihedral : 15.720 179.432 5580 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.07 % Favored : 94.68 % Rotamer: Outliers : 1.16 % Allowed : 7.92 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3532 helix: 0.71 (0.15), residues: 1226 sheet: -1.00 (0.21), residues: 594 loop : -1.27 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 152 TYR 0.027 0.001 TYR C 190 PHE 0.036 0.002 PHE C 343 TRP 0.021 0.002 TRP H 219 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (33142) covalent geometry : angle 0.64564 / 0.34 (45376) hydrogen bonds : bond 0.05638 / 3.78 ( 1055) hydrogen bonds : angle 5.69357 / 3.98 ( 2877) *********************** 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 351 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4322 (ttm) cc_final: 0.3984 (tpt) REVERT: A 287 MET cc_start: 0.5935 (mmm) cc_final: 0.5579 (mmm) REVERT: B 74 MET cc_start: 0.8501 (ppp) cc_final: 0.8183 (ppp) REVERT: C 190 TYR cc_start: 0.4538 (m-10) cc_final: 0.4218 (m-10) REVERT: E 40 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8343 (mtmt) REVERT: E 446 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8681 (t160) REVERT: E 484 ASP cc_start: 0.8296 (t70) cc_final: 0.7817 (t0) REVERT: F 190 TYR cc_start: 0.7389 (m-80) cc_final: 0.6703 (m-10) REVERT: F 192 TRP cc_start: 0.5732 (p-90) cc_final: 0.5447 (p-90) REVERT: F 317 LYS cc_start: 0.5521 (mttm) cc_final: 0.5212 (mtmm) REVERT: G 107 ASN cc_start: 0.7111 (t0) cc_final: 0.6531 (t0) REVERT: H 193 MET cc_start: 0.6187 (ttm) cc_final: 0.5893 (mmm) REVERT: H 308 THR cc_start: 0.6174 (OUTLIER) cc_final: 0.5927 (t) REVERT: M 151 CYS cc_start: 0.7378 (t) cc_final: 0.7077 (t) REVERT: M 245 PHE cc_start: 0.7316 (m-10) cc_final: 0.6966 (m-10) REVERT: M 406 LEU cc_start: 0.9072 (mm) cc_final: 0.8850 (mm) outliers start: 37 outliers final: 26 residues processed: 334 average time/residue: 0.1886 time to fit residues: 107.3928 Evaluate side-chains 301 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 104 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 358 optimal weight: 30.0000 chunk 308 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN F 226 HIS G 207 HIS G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 GLN G 329 HIS ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN M 329 HIS M 360 HIS M 430 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.116689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.093510 restraints weight = 87092.322| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.29 r_work: 0.3494 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33142 Z= 0.177 Angle : 0.615 9.415 45376 Z= 0.328 Chirality : 0.043 0.261 4984 Planarity : 0.005 0.082 5238 Dihedral : 15.742 178.007 5580 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.90 % Favored : 94.85 % Rotamer: Outliers : 1.75 % Allowed : 9.73 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3532 helix: 0.84 (0.15), residues: 1210 sheet: -0.93 (0.21), residues: 614 loop : -1.23 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 213 TYR 0.018 0.001 TYR M 280 PHE 0.025 0.002 PHE A 198 TRP 0.021 0.001 TRP E 370 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (33142) covalent geometry : angle 0.61455 / 0.33 (45376) hydrogen bonds : bond 0.05080 / 3.39 ( 1055) hydrogen bonds : angle 5.36149 / 3.75 ( 2877) *********************** 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 358 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (mm) REVERT: A 395 MET cc_start: 0.6120 (tpp) cc_final: 0.5299 (mmm) REVERT: B 74 MET cc_start: 0.8518 (ppp) cc_final: 0.8070 (ppp) REVERT: B 364 ARG cc_start: 0.7228 (mtm180) cc_final: 0.6917 (mtt180) REVERT: E 40 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8415 (mtmt) REVERT: E 484 ASP cc_start: 0.8238 (t70) cc_final: 0.7739 (t0) REVERT: F 190 TYR cc_start: 0.7460 (m-80) cc_final: 0.6804 (m-10) REVERT: F 193 MET cc_start: 0.2669 (tpp) cc_final: 0.2092 (tpp) REVERT: F 221 TYR cc_start: 0.7055 (m-80) cc_final: 0.6768 (m-80) REVERT: F 229 LYS cc_start: 0.6063 (ttmt) cc_final: 0.5288 (mmmt) REVERT: F 317 LYS cc_start: 0.5585 (mttm) cc_final: 0.5240 (mtmm) REVERT: F 391 PHE cc_start: 0.8925 (p90) cc_final: 0.8606 (p90) REVERT: G 1 MET cc_start: 0.6049 (mmp) cc_final: 0.5641 (mmm) REVERT: G 107 ASN cc_start: 0.6941 (t0) cc_final: 0.6423 (t0) REVERT: G 348 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: G 399 THR cc_start: 0.5736 (OUTLIER) cc_final: 0.5528 (p) REVERT: H 193 MET cc_start: 0.6119 (ttm) cc_final: 0.5902 (tpp) REVERT: H 308 THR cc_start: 0.6069 (OUTLIER) cc_final: 0.5796 (t) REVERT: H 320 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.6478 (m90) REVERT: M 151 CYS cc_start: 0.7011 (t) cc_final: 0.6757 (t) REVERT: M 245 PHE cc_start: 0.7276 (m-10) cc_final: 0.6940 (m-10) REVERT: M 406 LEU cc_start: 0.9125 (mm) cc_final: 0.8905 (mm) outliers start: 56 outliers final: 33 residues processed: 334 average time/residue: 0.1893 time to fit residues: 107.9185 Evaluate side-chains 309 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 165 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 357 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 330 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 333 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.115104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.092223 restraints weight = 87497.355| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.18 r_work: 0.3485 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33142 Z= 0.209 Angle : 0.636 9.353 45376 Z= 0.339 Chirality : 0.044 0.277 4984 Planarity : 0.005 0.075 5238 Dihedral : 15.827 177.221 5580 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.41 % Favored : 94.37 % Rotamer: Outliers : 2.25 % Allowed : 11.45 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3532 helix: 0.82 (0.15), residues: 1218 sheet: -1.02 (0.21), residues: 618 loop : -1.19 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 113 TYR 0.023 0.002 TYR M 280 PHE 0.022 0.002 PHE C 343 TRP 0.019 0.002 TRP E 370 HIS 0.009 0.002 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (33142) covalent geometry : angle 0.63630 / 0.34 (45376) hydrogen bonds : bond 0.05001 / 3.33 ( 1055) hydrogen bonds : angle 5.28525 / 3.71 ( 2877) *********************** 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 362 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 290 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 88 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8067 (mm) REVERT: A 193 MET cc_start: 0.4583 (ttm) cc_final: 0.4160 (tpp) REVERT: A 393 LEU cc_start: 0.8211 (tp) cc_final: 0.8007 (tp) REVERT: A 395 MET cc_start: 0.5922 (tpp) cc_final: 0.5619 (mtp) REVERT: A 401 VAL cc_start: 0.7811 (t) cc_final: 0.6680 (t) REVERT: B 74 MET cc_start: 0.8478 (ppp) cc_final: 0.8061 (ppp) REVERT: B 364 ARG cc_start: 0.7261 (mtm180) cc_final: 0.6927 (mtt180) REVERT: C 309 MET cc_start: 0.6808 (ptm) cc_final: 0.6575 (ptm) REVERT: E 40 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8525 (mtmt) REVERT: E 446 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (t160) REVERT: E 484 ASP cc_start: 0.8395 (t70) cc_final: 0.7864 (t0) REVERT: F 190 TYR cc_start: 0.7447 (m-80) cc_final: 0.6863 (m-10) REVERT: F 193 MET cc_start: 0.3362 (tpp) cc_final: 0.3080 (tpp) REVERT: F 229 LYS cc_start: 0.5693 (ttmt) cc_final: 0.4871 (mmmt) REVERT: F 317 LYS cc_start: 0.5622 (mttm) cc_final: 0.5245 (mtmm) REVERT: G 1 MET cc_start: 0.6080 (mmp) cc_final: 0.5586 (mmm) REVERT: G 107 ASN cc_start: 0.6922 (t0) cc_final: 0.6492 (t0) REVERT: G 348 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: H 193 MET cc_start: 0.6345 (ttm) cc_final: 0.5989 (tpp) REVERT: H 287 MET cc_start: 0.7205 (tpt) cc_final: 0.6782 (tpt) REVERT: H 308 THR cc_start: 0.6381 (OUTLIER) cc_final: 0.6115 (t) REVERT: H 320 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6798 (m90) REVERT: H 395 MET cc_start: 0.7157 (mmp) cc_final: 0.6944 (mmp) REVERT: M 151 CYS cc_start: 0.7065 (t) cc_final: 0.6639 (t) REVERT: M 245 PHE cc_start: 0.7541 (m-10) cc_final: 0.7271 (m-10) outliers start: 72 outliers final: 42 residues processed: 333 average time/residue: 0.1669 time to fit residues: 95.4622 Evaluate side-chains 311 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 157 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 270 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN E 296 ASN E 446 ASN F 226 HIS F 267 GLN G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.117485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.093862 restraints weight = 88543.248| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.32 r_work: 0.3515 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33142 Z= 0.129 Angle : 0.576 12.125 45376 Z= 0.306 Chirality : 0.043 0.245 4984 Planarity : 0.005 0.071 5238 Dihedral : 15.786 176.253 5580 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.76 % Rotamer: Outliers : 2.16 % Allowed : 13.08 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3532 helix: 1.05 (0.15), residues: 1206 sheet: -0.88 (0.21), residues: 634 loop : -1.17 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.018 0.001 TYR C 105 PHE 0.028 0.001 PHE G 365 TRP 0.022 0.001 TRP G 370 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (33142) covalent geometry : angle 0.57623 / 0.31 (45376) hydrogen bonds : bond 0.04366 / 2.92 ( 1055) hydrogen bonds : angle 5.09554 / 3.59 ( 2877) *********************** 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 375 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 306 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 287 MET cc_start: 0.5799 (mmm) cc_final: 0.5353 (mmm) REVERT: A 395 MET cc_start: 0.5754 (tpp) cc_final: 0.5474 (mtp) REVERT: A 401 VAL cc_start: 0.7779 (t) cc_final: 0.6567 (t) REVERT: B 74 MET cc_start: 0.8425 (ppp) cc_final: 0.7992 (ppp) REVERT: C 185 LEU cc_start: 0.9003 (tp) cc_final: 0.8763 (tp) REVERT: C 309 MET cc_start: 0.6796 (ptm) cc_final: 0.6580 (ptm) REVERT: C 341 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (mt) REVERT: C 364 GLN cc_start: 0.7823 (tm130) cc_final: 0.7479 (tm-30) REVERT: E 40 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8537 (mtmt) REVERT: E 446 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8464 (t160) REVERT: E 484 ASP cc_start: 0.8240 (t70) cc_final: 0.7752 (t0) REVERT: F 172 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7165 (p0) REVERT: F 190 TYR cc_start: 0.7376 (m-80) cc_final: 0.6788 (m-10) REVERT: F 229 LYS cc_start: 0.5963 (ttmt) cc_final: 0.5139 (mmmt) REVERT: F 317 LYS cc_start: 0.5544 (mttm) cc_final: 0.5180 (mtmm) REVERT: G 1 MET cc_start: 0.5976 (mmp) cc_final: 0.5642 (mmm) REVERT: G 107 ASN cc_start: 0.6929 (t0) cc_final: 0.6383 (t0) REVERT: G 348 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: H 193 MET cc_start: 0.6033 (ttm) cc_final: 0.5650 (tpp) REVERT: H 287 MET cc_start: 0.7218 (tpt) cc_final: 0.6617 (tpt) REVERT: H 308 THR cc_start: 0.6347 (OUTLIER) cc_final: 0.6012 (t) REVERT: H 320 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6722 (m90) REVERT: M 151 CYS cc_start: 0.7053 (t) cc_final: 0.6623 (t) REVERT: M 245 PHE cc_start: 0.7486 (m-10) cc_final: 0.7227 (m-10) REVERT: M 406 LEU cc_start: 0.8886 (mm) cc_final: 0.8669 (mm) outliers start: 69 outliers final: 38 residues processed: 349 average time/residue: 0.1761 time to fit residues: 104.4249 Evaluate side-chains 315 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 298 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 167 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 226 HIS ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.116284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.092726 restraints weight = 88644.794| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.30 r_work: 0.3495 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33142 Z= 0.162 Angle : 0.594 9.790 45376 Z= 0.315 Chirality : 0.043 0.234 4984 Planarity : 0.005 0.071 5238 Dihedral : 15.774 175.800 5580 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.27 % Favored : 94.54 % Rotamer: Outliers : 2.25 % Allowed : 14.08 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3532 helix: 1.05 (0.15), residues: 1206 sheet: -0.95 (0.21), residues: 638 loop : -1.18 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 126 TYR 0.017 0.001 TYR M 280 PHE 0.018 0.002 PHE A 198 TRP 0.020 0.001 TRP G 370 HIS 0.009 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (33142) covalent geometry : angle 0.59440 / 0.31 (45376) hydrogen bonds : bond 0.04470 / 2.97 ( 1055) hydrogen bonds : angle 5.08221 / 3.58 ( 2877) *********************** 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 348 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 193 MET cc_start: 0.4186 (ttm) cc_final: 0.3727 (tpt) REVERT: A 401 VAL cc_start: 0.7810 (t) cc_final: 0.6685 (t) REVERT: B 74 MET cc_start: 0.8394 (ppp) cc_final: 0.7952 (ppp) REVERT: C 364 GLN cc_start: 0.7888 (tm130) cc_final: 0.7518 (tm-30) REVERT: E 40 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8537 (mtmt) REVERT: E 433 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.4718 (pp) REVERT: E 484 ASP cc_start: 0.8267 (t70) cc_final: 0.7791 (t0) REVERT: F 190 TYR cc_start: 0.7182 (m-80) cc_final: 0.6769 (m-10) REVERT: F 193 MET cc_start: 0.1811 (tpp) cc_final: 0.1447 (tpp) REVERT: F 229 LYS cc_start: 0.5959 (ttmt) cc_final: 0.5359 (mmmt) REVERT: F 317 LYS cc_start: 0.5583 (mttm) cc_final: 0.5183 (mtmm) REVERT: G 1 MET cc_start: 0.5995 (mmp) cc_final: 0.5711 (mmm) REVERT: G 107 ASN cc_start: 0.6877 (t0) cc_final: 0.6407 (t0) REVERT: G 348 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: H 193 MET cc_start: 0.6310 (ttm) cc_final: 0.5964 (tpp) REVERT: H 308 THR cc_start: 0.6383 (OUTLIER) cc_final: 0.6060 (t) REVERT: H 320 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6778 (m90) REVERT: M 151 CYS cc_start: 0.6980 (t) cc_final: 0.6661 (t) REVERT: M 245 PHE cc_start: 0.7557 (m-10) cc_final: 0.7341 (m-10) REVERT: M 406 LEU cc_start: 0.9039 (mm) cc_final: 0.8795 (mm) outliers start: 72 outliers final: 53 residues processed: 324 average time/residue: 0.1851 time to fit residues: 102.3100 Evaluate side-chains 320 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 329 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 226 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.112643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.089242 restraints weight = 89819.695| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.27 r_work: 0.3425 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 33142 Z= 0.293 Angle : 0.706 10.641 45376 Z= 0.372 Chirality : 0.046 0.248 4984 Planarity : 0.005 0.071 5238 Dihedral : 15.971 177.427 5580 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.12 % Favored : 93.69 % Rotamer: Outliers : 3.07 % Allowed : 13.77 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3532 helix: 0.84 (0.15), residues: 1184 sheet: -1.40 (0.21), residues: 608 loop : -1.23 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 72 TYR 0.024 0.002 TYR M 280 PHE 0.030 0.002 PHE E 104 TRP 0.018 0.002 TRP E 370 HIS 0.010 0.002 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.29 (33142) covalent geometry : angle 0.70617 / 0.37 (45376) hydrogen bonds : bond 0.05316 / 3.52 ( 1055) hydrogen bonds : angle 5.37317 / 3.78 ( 2877) *********************** 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 356 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 258 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 193 MET cc_start: 0.4101 (ttm) cc_final: 0.3820 (tpp) REVERT: A 395 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5561 (mtp) REVERT: B 74 MET cc_start: 0.8519 (ppp) cc_final: 0.8057 (ppp) REVERT: B 356 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 103 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6743 (tt) REVERT: C 309 MET cc_start: 0.6792 (ptm) cc_final: 0.6549 (ptm) REVERT: E 364 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8183 (ptp-170) REVERT: E 433 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5238 (pp) REVERT: E 484 ASP cc_start: 0.8301 (t70) cc_final: 0.7793 (t0) REVERT: F 136 GLU cc_start: 0.8566 (mp0) cc_final: 0.8264 (mp0) REVERT: F 190 TYR cc_start: 0.7261 (m-80) cc_final: 0.6894 (m-10) REVERT: F 193 MET cc_start: 0.1889 (tpp) cc_final: 0.1351 (tpp) REVERT: F 229 LYS cc_start: 0.5864 (ttmt) cc_final: 0.5213 (mmmt) REVERT: G 1 MET cc_start: 0.6065 (mmp) cc_final: 0.5555 (mmm) REVERT: G 107 ASN cc_start: 0.6965 (t0) cc_final: 0.6458 (t0) REVERT: G 348 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: H 308 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6220 (t) REVERT: H 320 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.6901 (m90) REVERT: M 406 LEU cc_start: 0.9074 (mm) cc_final: 0.8841 (mm) outliers start: 98 outliers final: 64 residues processed: 322 average time/residue: 0.1844 time to fit residues: 103.0089 Evaluate side-chains 313 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 241 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 422 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 245 GLU Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 314 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 58 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 321 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN C 226 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.114771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.091740 restraints weight = 87611.228| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.25 r_work: 0.3467 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33142 Z= 0.139 Angle : 0.605 12.151 45376 Z= 0.319 Chirality : 0.043 0.227 4984 Planarity : 0.005 0.068 5238 Dihedral : 15.894 176.914 5580 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.44 % Favored : 94.42 % Rotamer: Outliers : 2.19 % Allowed : 14.99 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3532 helix: 1.13 (0.15), residues: 1172 sheet: -1.13 (0.21), residues: 614 loop : -1.22 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 126 TYR 0.018 0.001 TYR G 65 PHE 0.033 0.002 PHE M 104 TRP 0.019 0.001 TRP E 370 HIS 0.008 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (33142) covalent geometry : angle 0.60488 / 0.32 (45376) hydrogen bonds : bond 0.04336 / 2.89 ( 1055) hydrogen bonds : angle 5.13651 / 3.62 ( 2877) *********************** 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 347 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 193 MET cc_start: 0.4485 (ttm) cc_final: 0.4192 (tpp) REVERT: A 287 MET cc_start: 0.5952 (mmm) cc_final: 0.5417 (mmm) REVERT: B 356 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 122 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7134 (ppp) REVERT: C 364 GLN cc_start: 0.7915 (tm130) cc_final: 0.7676 (tm-30) REVERT: E 484 ASP cc_start: 0.8205 (t70) cc_final: 0.7674 (t0) REVERT: F 136 GLU cc_start: 0.8377 (mp0) cc_final: 0.8086 (mp0) REVERT: F 190 TYR cc_start: 0.7224 (m-80) cc_final: 0.6820 (m-10) REVERT: F 193 MET cc_start: 0.1765 (tpp) cc_final: 0.1316 (tpp) REVERT: F 229 LYS cc_start: 0.5716 (ttmt) cc_final: 0.5142 (mmmt) REVERT: F 309 MET cc_start: 0.6826 (tmm) cc_final: 0.6561 (tmm) REVERT: G 1 MET cc_start: 0.5889 (mmp) cc_final: 0.5531 (mmm) REVERT: G 107 ASN cc_start: 0.6880 (t0) cc_final: 0.6361 (t0) REVERT: G 350 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7263 (mm) REVERT: H 308 THR cc_start: 0.6183 (OUTLIER) cc_final: 0.5875 (t) REVERT: H 320 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6708 (m90) REVERT: M 406 LEU cc_start: 0.9108 (mm) cc_final: 0.8854 (mm) outliers start: 70 outliers final: 47 residues processed: 321 average time/residue: 0.1847 time to fit residues: 102.2401 Evaluate side-chains 313 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 342 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 281 optimal weight: 8.9990 chunk 351 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.115599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092659 restraints weight = 87082.636| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.22 r_work: 0.3484 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33142 Z= 0.131 Angle : 0.595 12.334 45376 Z= 0.313 Chirality : 0.043 0.334 4984 Planarity : 0.005 0.067 5238 Dihedral : 15.817 175.788 5580 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 2.00 % Allowed : 15.64 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3532 helix: 1.16 (0.15), residues: 1192 sheet: -0.98 (0.21), residues: 628 loop : -1.17 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 263 TYR 0.019 0.001 TYR H 330 PHE 0.027 0.001 PHE H 305 TRP 0.019 0.001 TRP E 370 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (33142) covalent geometry : angle 0.59510 / 0.31 (45376) hydrogen bonds : bond 0.04186 / 2.77 ( 1055) hydrogen bonds : angle 5.06457 / 3.58 ( 2877) *********************** 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 349 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 285 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8115 (mm) REVERT: A 287 MET cc_start: 0.6057 (mmm) cc_final: 0.5525 (mmm) REVERT: B 356 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 57 THR cc_start: 0.8478 (m) cc_final: 0.8224 (m) REVERT: C 76 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8353 (ttmm) REVERT: C 364 GLN cc_start: 0.7890 (tm130) cc_final: 0.7674 (tm-30) REVERT: E 285 TYR cc_start: 0.8768 (m-80) cc_final: 0.8191 (m-10) REVERT: E 446 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8767 (t160) REVERT: E 484 ASP cc_start: 0.8064 (t70) cc_final: 0.7543 (t0) REVERT: F 136 GLU cc_start: 0.8411 (mp0) cc_final: 0.8100 (mp0) REVERT: F 190 TYR cc_start: 0.7193 (m-80) cc_final: 0.6831 (m-10) REVERT: F 193 MET cc_start: 0.2309 (tpp) cc_final: 0.1897 (tpp) REVERT: F 229 LYS cc_start: 0.5714 (ttmt) cc_final: 0.5141 (mmmt) REVERT: F 309 MET cc_start: 0.6832 (tmm) cc_final: 0.6550 (tmm) REVERT: F 323 ILE cc_start: 0.9006 (pt) cc_final: 0.8791 (mt) REVERT: G 1 MET cc_start: 0.5845 (mmp) cc_final: 0.5446 (mmm) REVERT: G 107 ASN cc_start: 0.6841 (t0) cc_final: 0.6347 (t0) REVERT: H 212 ASN cc_start: 0.7663 (p0) cc_final: 0.7196 (p0) REVERT: H 254 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: H 308 THR cc_start: 0.6083 (OUTLIER) cc_final: 0.5762 (t) REVERT: H 320 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.6629 (m90) REVERT: M 406 LEU cc_start: 0.9104 (mm) cc_final: 0.8838 (mm) outliers start: 64 outliers final: 47 residues processed: 325 average time/residue: 0.1828 time to fit residues: 102.8745 Evaluate side-chains 322 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 311 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 340 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 259 optimal weight: 0.7980 chunk 319 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.113706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.090863 restraints weight = 88020.174| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.21 r_work: 0.3449 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33142 Z= 0.200 Angle : 0.640 11.929 45376 Z= 0.335 Chirality : 0.044 0.231 4984 Planarity : 0.005 0.068 5238 Dihedral : 15.850 176.258 5580 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.05 % Rotamer: Outliers : 2.00 % Allowed : 15.71 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3532 helix: 1.12 (0.15), residues: 1190 sheet: -1.08 (0.21), residues: 640 loop : -1.21 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 263 TYR 0.020 0.001 TYR M 280 PHE 0.019 0.002 PHE G 419 TRP 0.025 0.002 TRP M 421 HIS 0.008 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (33142) covalent geometry : angle 0.63959 / 0.34 (45376) hydrogen bonds : bond 0.04605 / 3.04 ( 1055) hydrogen bonds : angle 5.18255 / 3.66 ( 2877) ********************** 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 332 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 287 MET cc_start: 0.6210 (mmm) cc_final: 0.5705 (mmm) REVERT: B 13 LEU cc_start: 0.7929 (tp) cc_final: 0.7697 (tp) REVERT: B 356 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 57 THR cc_start: 0.8525 (m) cc_final: 0.8262 (m) REVERT: C 364 GLN cc_start: 0.7990 (tm130) cc_final: 0.7687 (tm-30) REVERT: E 484 ASP cc_start: 0.8085 (t70) cc_final: 0.7546 (t0) REVERT: F 136 GLU cc_start: 0.8379 (mp0) cc_final: 0.8096 (mp0) REVERT: F 190 TYR cc_start: 0.7240 (m-80) cc_final: 0.6886 (m-10) REVERT: F 193 MET cc_start: 0.2408 (tpp) cc_final: 0.1984 (tpp) REVERT: F 229 LYS cc_start: 0.6062 (ttmt) cc_final: 0.5418 (mmmt) REVERT: F 309 MET cc_start: 0.6593 (tmm) cc_final: 0.6326 (tmm) REVERT: F 323 ILE cc_start: 0.9033 (pt) cc_final: 0.8805 (mt) REVERT: G 1 MET cc_start: 0.5901 (mmp) cc_final: 0.5266 (mmm) REVERT: G 107 ASN cc_start: 0.6848 (t0) cc_final: 0.6370 (t0) REVERT: H 212 ASN cc_start: 0.7738 (p0) cc_final: 0.7266 (p0) REVERT: H 308 THR cc_start: 0.6083 (OUTLIER) cc_final: 0.5716 (t) REVERT: H 320 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6666 (m90) REVERT: M 406 LEU cc_start: 0.9148 (mm) cc_final: 0.8885 (mm) outliers start: 64 outliers final: 50 residues processed: 308 average time/residue: 0.1749 time to fit residues: 94.0298 Evaluate side-chains 317 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 332 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 226 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 357 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.114464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091659 restraints weight = 87633.438| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.21 r_work: 0.3469 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33142 Z= 0.159 Angle : 0.612 12.055 45376 Z= 0.319 Chirality : 0.043 0.222 4984 Planarity : 0.005 0.067 5238 Dihedral : 15.847 176.060 5580 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 1.97 % Allowed : 16.08 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3532 helix: 1.17 (0.15), residues: 1190 sheet: -1.07 (0.21), residues: 634 loop : -1.21 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 263 TYR 0.017 0.001 TYR H 330 PHE 0.027 0.002 PHE H 332 TRP 0.018 0.001 TRP M 421 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (33142) covalent geometry : angle 0.61234 / 0.32 (45376) hydrogen bonds : bond 0.04283 / 2.83 ( 1055) hydrogen bonds : angle 5.12298 / 3.62 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7453.28 seconds wall clock time: 129 minutes 21.27 seconds (7761.27 seconds total)