Starting phenix.real_space_refine on Tue Aug 26 03:41:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozg_17308/08_2025/8ozg_17308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozg_17308/08_2025/8ozg_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ozg_17308/08_2025/8ozg_17308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozg_17308/08_2025/8ozg_17308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozg_17308/08_2025/8ozg_17308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozg_17308/08_2025/8ozg_17308.map" } 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-2.0-5787/lib/python3.9/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: 6.05, per 1000 atoms: 0.19 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 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: 3.50 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: 5.50 Time building geometry restraints manager: 3.26 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: 45103 3.35 - 6.70: 245 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: 19185 33.71 - 67.42: 794 67.42 - 101.12: 44 101.12 - 134.83: 4 134.83 - 168.54: 13 Dihedral angle restraints: 20040 sinusoidal: 9532 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 20037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4785 0.096 - 0.191: 193 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.540 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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= 0.298 Angle : 0.727 16.758 45376 Z= 0.414 Chirality : 0.042 0.478 4984 Planarity : 0.005 0.146 5238 Dihedral : 17.233 168.539 13248 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 aren 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 covalent geometry : bond 0.00600 (33142) covalent geometry : angle 0.72669 (45376) hydrogen bonds : bond 0.18812 ( 1055) hydrogen bonds : angle 7.36024 ( 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 : 1.095 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: 0.1722 time to fit residues: 122.8515 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 : 0.835 ------------------------------------------------------------------------------- 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: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 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 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 35 ASN M 360 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.119523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.095802 restraints weight = 88311.194| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.33 r_work: 0.3548 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33142 Z= 0.170 Angle : 0.630 11.053 45376 Z= 0.333 Chirality : 0.043 0.295 4984 Planarity : 0.005 0.101 5238 Dihedral : 17.678 179.250 5960 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.04 % Favored : 94.71 % Rotamer: Outliers : 1.28 % Allowed : 7.63 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.14), residues: 3532 helix: 0.81 (0.15), residues: 1222 sheet: -0.91 (0.21), residues: 614 loop : -1.25 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 152 TYR 0.018 0.001 TYR C 190 PHE 0.034 0.002 PHE A 17 TRP 0.020 0.001 TRP E 370 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00384 (33142) covalent geometry : angle 0.63042 (45376) hydrogen bonds : bond 0.05226 ( 1055) hydrogen bonds : angle 5.47931 ( 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 361 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 0.876 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: A 287 MET cc_start: 0.6041 (mmm) cc_final: 0.5654 (mmm) REVERT: A 395 MET cc_start: 0.6127 (tpp) cc_final: 0.5698 (mtp) REVERT: A 401 VAL cc_start: 0.7730 (t) cc_final: 0.6680 (t) REVERT: B 74 MET cc_start: 0.8455 (ppp) cc_final: 0.8079 (ppp) REVERT: B 85 LYS cc_start: 0.8660 (mttt) cc_final: 0.8319 (mtmt) REVERT: B 364 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6781 (mtt180) REVERT: E 40 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8382 (mtmt) REVERT: E 106 TYR cc_start: 0.7445 (m-10) cc_final: 0.7229 (m-10) REVERT: E 446 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8710 (t160) REVERT: E 476 GLU cc_start: 0.8407 (tt0) cc_final: 0.8096 (tt0) REVERT: E 484 ASP cc_start: 0.8132 (t70) cc_final: 0.7711 (t0) REVERT: F 190 TYR cc_start: 0.7334 (m-80) cc_final: 0.6730 (m-10) REVERT: F 192 TRP cc_start: 0.5773 (p-90) cc_final: 0.5553 (p-90) REVERT: F 221 TYR cc_start: 0.6930 (m-80) cc_final: 0.6570 (m-80) REVERT: F 277 MET cc_start: 0.6868 (mmt) cc_final: 0.6616 (mmm) REVERT: F 317 LYS cc_start: 0.5497 (mttm) cc_final: 0.5187 (mtmm) REVERT: H 193 MET cc_start: 0.6228 (ttm) cc_final: 0.5944 (mmm) REVERT: H 308 THR cc_start: 0.6216 (OUTLIER) cc_final: 0.5952 (t) REVERT: H 320 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6480 (m90) REVERT: H 381 ILE cc_start: 0.7632 (mt) cc_final: 0.7207 (pt) REVERT: M 151 CYS cc_start: 0.7186 (t) cc_final: 0.6919 (t) REVERT: M 245 PHE cc_start: 0.7266 (m-10) cc_final: 0.6985 (m-10) REVERT: M 406 LEU cc_start: 0.9098 (mm) cc_final: 0.8883 (mm) outliers start: 41 outliers final: 28 residues processed: 343 average time/residue: 0.1535 time to fit residues: 89.5331 Evaluate side-chains 297 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 426 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 329 LEU 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 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain H residue 8 SER 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 35 ASN 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: 6.9990 chunk 214 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 238 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** 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 ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN M 61 GLN M 329 HIS M 430 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.112010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.088778 restraints weight = 88281.340| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.25 r_work: 0.3409 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 33142 Z= 0.283 Angle : 0.731 9.207 45376 Z= 0.386 Chirality : 0.047 0.303 4984 Planarity : 0.006 0.087 5238 Dihedral : 17.939 178.674 5960 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 2.57 % Allowed : 10.86 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 3532 helix: 0.58 (0.15), residues: 1196 sheet: -1.15 (0.22), residues: 570 loop : -1.22 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 152 TYR 0.028 0.002 TYR M 280 PHE 0.027 0.003 PHE A 17 TRP 0.024 0.002 TRP E 370 HIS 0.009 0.002 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00645 (33142) covalent geometry : angle 0.73135 (45376) hydrogen bonds : bond 0.05648 ( 1055) hydrogen bonds : angle 5.50563 ( 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 368 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 286 time to evaluate : 1.113 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: 0.8459 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 393 LEU cc_start: 0.8164 (tp) cc_final: 0.7472 (tp) REVERT: B 13 LEU cc_start: 0.7915 (tp) cc_final: 0.7710 (tp) REVERT: B 74 MET cc_start: 0.8583 (ppp) cc_final: 0.8105 (ppp) REVERT: B 85 LYS cc_start: 0.9087 (mttt) cc_final: 0.8848 (mttp) REVERT: B 364 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7267 (mtt180) REVERT: C 309 MET cc_start: 0.6839 (ptm) cc_final: 0.6600 (ptm) REVERT: E 40 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8473 (mtmt) REVERT: E 61 GLN cc_start: 0.8731 (mp10) cc_final: 0.8526 (mp10) REVERT: E 476 GLU cc_start: 0.8421 (tt0) cc_final: 0.8086 (tt0) REVERT: E 484 ASP cc_start: 0.8426 (t70) cc_final: 0.7826 (t0) REVERT: F 190 TYR cc_start: 0.7397 (m-80) cc_final: 0.6829 (m-80) REVERT: F 192 TRP cc_start: 0.5840 (p-90) cc_final: 0.5596 (p-90) REVERT: F 406 GLU cc_start: 0.6397 (tm-30) cc_final: 0.6173 (tm-30) REVERT: G 1 MET cc_start: 0.6007 (mmp) cc_final: 0.5320 (mmt) REVERT: G 107 ASN cc_start: 0.6920 (t0) cc_final: 0.6428 (t0) REVERT: G 348 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: H 287 MET cc_start: 0.7040 (tpt) cc_final: 0.6217 (tpt) REVERT: H 308 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6448 (t) REVERT: H 320 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6792 (m90) REVERT: H 381 ILE cc_start: 0.7580 (mt) cc_final: 0.7111 (pt) REVERT: M 245 PHE cc_start: 0.7721 (m-10) cc_final: 0.7485 (m-10) REVERT: M 406 LEU cc_start: 0.9131 (mm) cc_final: 0.8906 (mm) outliers start: 82 outliers final: 47 residues processed: 343 average time/residue: 0.1633 time to fit residues: 95.0760 Evaluate side-chains 303 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 179 LEU 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 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 399 THR 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 264 LEU Chi-restraints excluded: chain C residue 320 HIS 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 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 181 PHE 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 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 245 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 165 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 270 ASN ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN F 267 GLN G 207 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.114166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.091131 restraints weight = 87391.764| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.27 r_work: 0.3451 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33142 Z= 0.154 Angle : 0.596 10.530 45376 Z= 0.316 Chirality : 0.042 0.251 4984 Planarity : 0.005 0.079 5238 Dihedral : 17.814 177.968 5960 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 2.41 % Allowed : 13.08 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3532 helix: 0.91 (0.15), residues: 1184 sheet: -0.97 (0.20), residues: 632 loop : -1.21 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 126 TYR 0.023 0.001 TYR C 190 PHE 0.024 0.002 PHE A 198 TRP 0.020 0.001 TRP E 370 HIS 0.009 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00348 (33142) covalent geometry : angle 0.59607 (45376) hydrogen bonds : bond 0.04534 ( 1055) hydrogen bonds : angle 5.17467 ( 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 369 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 88 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7827 (mm) REVERT: B 74 MET cc_start: 0.8399 (ppp) cc_final: 0.7930 (ppp) REVERT: B 85 LYS cc_start: 0.9073 (mttt) cc_final: 0.8826 (mttp) REVERT: B 356 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7416 (tm-30) REVERT: C 266 VAL cc_start: 0.8776 (t) cc_final: 0.8512 (m) REVERT: E 40 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8491 (mtmt) REVERT: E 476 GLU cc_start: 0.8452 (tt0) cc_final: 0.8112 (tt0) REVERT: E 484 ASP cc_start: 0.8221 (t70) cc_final: 0.7695 (t0) REVERT: F 190 TYR cc_start: 0.7349 (m-80) cc_final: 0.6736 (m-80) REVERT: F 323 ILE cc_start: 0.8927 (pt) cc_final: 0.8725 (mt) REVERT: F 406 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6164 (tm-30) REVERT: G 1 MET cc_start: 0.5735 (mmp) cc_final: 0.5517 (mmm) REVERT: G 107 ASN cc_start: 0.6942 (t0) cc_final: 0.6402 (t0) REVERT: G 348 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: H 287 MET cc_start: 0.7056 (tpt) cc_final: 0.6635 (tpt) REVERT: H 308 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6384 (t) REVERT: H 320 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6681 (m90) REVERT: H 381 ILE cc_start: 0.7674 (mt) cc_final: 0.7315 (pt) REVERT: M 245 PHE cc_start: 0.7687 (m-10) cc_final: 0.7438 (m-10) outliers start: 77 outliers final: 43 residues processed: 348 average time/residue: 0.1581 time to fit residues: 93.2964 Evaluate side-chains 310 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 111 HIS Chi-restraints excluded: chain B residue 147 ILE 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 131 ILE Chi-restraints excluded: chain C residue 156 GLN 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 137 ASP 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 157 ILE 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 201 optimal weight: 0.0870 chunk 130 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 109 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN E 296 ASN E 446 ASN G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 357 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.115901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.093138 restraints weight = 87388.477| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.19 r_work: 0.3505 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33142 Z= 0.128 Angle : 0.576 10.075 45376 Z= 0.303 Chirality : 0.042 0.222 4984 Planarity : 0.005 0.075 5238 Dihedral : 17.668 177.076 5960 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.78 % Favored : 95.02 % Rotamer: Outliers : 2.32 % Allowed : 14.14 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.14), residues: 3532 helix: 1.05 (0.15), residues: 1200 sheet: -0.95 (0.20), residues: 644 loop : -1.18 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 364 TYR 0.016 0.001 TYR C 190 PHE 0.028 0.001 PHE E 104 TRP 0.019 0.001 TRP E 370 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00286 (33142) covalent geometry : angle 0.57583 (45376) hydrogen bonds : bond 0.04146 ( 1055) hydrogen bonds : angle 5.01596 ( 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 376 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 302 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.5826 (mmm) cc_final: 0.5438 (mmm) REVERT: A 314 GLN cc_start: 0.5314 (tt0) cc_final: 0.4894 (tm-30) REVERT: A 393 LEU cc_start: 0.8211 (tp) cc_final: 0.7821 (tp) REVERT: B 356 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 57 THR cc_start: 0.8408 (m) cc_final: 0.8155 (m) REVERT: C 185 LEU cc_start: 0.8943 (tp) cc_final: 0.8729 (tp) REVERT: E 40 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8549 (mtmt) REVERT: E 476 GLU cc_start: 0.8363 (tt0) cc_final: 0.8076 (tt0) REVERT: E 484 ASP cc_start: 0.8184 (t70) cc_final: 0.7683 (t0) REVERT: F 136 GLU cc_start: 0.8384 (mp0) cc_final: 0.8075 (mp0) REVERT: F 190 TYR cc_start: 0.7228 (m-80) cc_final: 0.6967 (m-80) REVERT: F 317 LYS cc_start: 0.5603 (mttm) cc_final: 0.5154 (mtmm) REVERT: F 406 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6377 (tm-30) REVERT: G 1 MET cc_start: 0.5702 (mmp) cc_final: 0.5373 (mmm) REVERT: G 107 ASN cc_start: 0.6963 (t0) cc_final: 0.6435 (t0) REVERT: H 254 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7332 (m-40) REVERT: H 308 THR cc_start: 0.6630 (OUTLIER) cc_final: 0.6355 (t) REVERT: H 320 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6646 (m90) REVERT: H 381 ILE cc_start: 0.7716 (mt) cc_final: 0.7337 (pt) outliers start: 74 outliers final: 43 residues processed: 350 average time/residue: 0.1651 time to fit residues: 97.4221 Evaluate side-chains 312 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain A residue 401 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 229 LEU 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 156 GLN 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 118 VAL 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 15 ASN 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 G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 422 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 158 PHE 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 223 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 298 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 HIS ** 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** ** 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 = 0.3999 r_free = 0.3999 target = 0.114145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091278 restraints weight = 87490.469| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.20 r_work: 0.3461 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33142 Z= 0.175 Angle : 0.608 14.811 45376 Z= 0.317 Chirality : 0.043 0.225 4984 Planarity : 0.005 0.072 5238 Dihedral : 17.648 177.281 5960 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.28 % Rotamer: Outliers : 2.91 % Allowed : 14.49 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3532 helix: 1.03 (0.15), residues: 1192 sheet: -0.92 (0.20), residues: 638 loop : -1.20 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 54 TYR 0.019 0.001 TYR M 150 PHE 0.025 0.002 PHE G 365 TRP 0.037 0.001 TRP G 370 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00400 (33142) covalent geometry : angle 0.60834 (45376) hydrogen bonds : bond 0.04451 ( 1055) hydrogen bonds : angle 5.05738 ( 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 370 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 277 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 393 LEU cc_start: 0.8212 (tp) cc_final: 0.8003 (tp) REVERT: B 13 LEU cc_start: 0.7765 (tp) cc_final: 0.7558 (tp) REVERT: B 356 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 37 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8834 (tt) REVERT: C 57 THR cc_start: 0.8514 (m) cc_final: 0.8269 (m) REVERT: E 40 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8500 (mtmt) REVERT: E 72 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5975 (mtt-85) REVERT: E 476 GLU cc_start: 0.8415 (tt0) cc_final: 0.8150 (tt0) REVERT: E 484 ASP cc_start: 0.8183 (t70) cc_final: 0.7674 (t0) REVERT: F 190 TYR cc_start: 0.7213 (m-80) cc_final: 0.6867 (m-80) REVERT: F 193 MET cc_start: 0.1722 (tpp) cc_final: 0.1082 (tpp) REVERT: F 229 LYS cc_start: 0.5654 (ttmt) cc_final: 0.5188 (mmmt) REVERT: F 309 MET cc_start: 0.6638 (tmm) cc_final: 0.6395 (tmm) REVERT: F 406 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6436 (tm-30) REVERT: G 1 MET cc_start: 0.5701 (mmp) cc_final: 0.5388 (mmm) REVERT: G 107 ASN cc_start: 0.6957 (t0) cc_final: 0.6430 (t0) REVERT: H 212 ASN cc_start: 0.7633 (p0) cc_final: 0.7186 (p0) REVERT: H 254 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7257 (m-40) REVERT: H 308 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6400 (t) REVERT: H 320 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.6627 (m90) REVERT: H 381 ILE cc_start: 0.7718 (mt) cc_final: 0.7346 (pt) outliers start: 93 outliers final: 60 residues processed: 340 average time/residue: 0.1630 time to fit residues: 94.4450 Evaluate side-chains 329 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 340 HIS 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 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 279 CYS Chi-restraints excluded: chain B residue 329 HIS 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 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 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 72 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 118 VAL 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 15 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 136 GLU 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 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 221 THR Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 405 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 161 MET 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 494 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 329 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 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** ** 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 = 0.3988 r_free = 0.3988 target = 0.113470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.090635 restraints weight = 87912.168| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.21 r_work: 0.3447 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3190 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= 0.183 Angle : 0.608 10.447 45376 Z= 0.319 Chirality : 0.043 0.221 4984 Planarity : 0.005 0.071 5238 Dihedral : 17.642 177.320 5960 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 2.94 % Allowed : 14.89 % Favored : 82.17 % 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 aren not related in a simple way. whole: -0.60 (0.14), residues: 3532 helix: 1.05 (0.15), residues: 1192 sheet: -0.99 (0.20), residues: 636 loop : -1.18 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 263 TYR 0.017 0.001 TYR B 56 PHE 0.018 0.002 PHE A 198 TRP 0.022 0.001 TRP G 370 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00421 (33142) covalent geometry : angle 0.60844 (45376) hydrogen bonds : bond 0.04448 ( 1055) hydrogen bonds : angle 5.09983 ( 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 362 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 268 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7791 (mm) REVERT: B 13 LEU cc_start: 0.7737 (tp) cc_final: 0.7526 (tp) REVERT: B 356 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 403 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.4045 (m-10) REVERT: C 57 THR cc_start: 0.8527 (m) cc_final: 0.8268 (m) REVERT: E 40 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8512 (mtmt) REVERT: E 72 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6054 (mtt-85) REVERT: E 104 PHE cc_start: 0.6253 (m-80) cc_final: 0.5956 (t80) REVERT: E 364 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8200 (ptp-170) REVERT: E 476 GLU cc_start: 0.8408 (tt0) cc_final: 0.8128 (tt0) REVERT: E 484 ASP cc_start: 0.8211 (t70) cc_final: 0.7702 (t0) REVERT: F 46 TRP cc_start: 0.7058 (OUTLIER) cc_final: 0.6381 (t60) REVERT: F 190 TYR cc_start: 0.7239 (m-80) cc_final: 0.6591 (m-80) REVERT: F 193 MET cc_start: 0.1803 (tpp) cc_final: 0.0935 (tpp) REVERT: F 229 LYS cc_start: 0.5691 (ttmt) cc_final: 0.5228 (mmmt) REVERT: F 323 ILE cc_start: 0.9031 (pt) cc_final: 0.8783 (mt) REVERT: F 406 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6475 (tm-30) REVERT: G 1 MET cc_start: 0.5770 (mmp) cc_final: 0.5390 (mmm) REVERT: G 107 ASN cc_start: 0.6836 (t0) cc_final: 0.6305 (t0) REVERT: G 148 TYR cc_start: 0.8026 (t80) cc_final: 0.7144 (t80) REVERT: H 212 ASN cc_start: 0.7753 (p0) cc_final: 0.7314 (p0) REVERT: H 254 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7182 (m-40) REVERT: H 308 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6293 (t) REVERT: H 320 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6674 (m90) REVERT: H 381 ILE cc_start: 0.7721 (mt) cc_final: 0.7353 (pt) REVERT: H 395 MET cc_start: 0.7111 (mmp) cc_final: 0.6824 (mmp) REVERT: M 161 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3723 (ptm) REVERT: M 273 ASP cc_start: 0.8242 (m-30) cc_final: 0.7570 (p0) outliers start: 94 outliers final: 68 residues processed: 330 average time/residue: 0.1511 time to fit residues: 85.4329 Evaluate side-chains 335 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 178 ILE Chi-restraints excluded: chain A residue 340 HIS 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 229 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 405 ILE 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 156 GLN Chi-restraints excluded: chain C residue 164 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 C residue 406 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 ASP 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 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 136 GLU 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 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 221 THR Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 405 ILE 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 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 158 PHE 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 161 MET Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 350 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: 6.9990 chunk 202 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 332 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 321 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 222 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.112793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.089892 restraints weight = 88030.042| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.21 r_work: 0.3433 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33142 Z= 0.195 Angle : 0.617 9.998 45376 Z= 0.323 Chirality : 0.043 0.213 4984 Planarity : 0.005 0.070 5238 Dihedral : 17.649 177.148 5960 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.89 % Favored : 93.91 % Rotamer: Outliers : 2.88 % Allowed : 15.64 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.14), residues: 3532 helix: 1.03 (0.15), residues: 1196 sheet: -1.11 (0.20), residues: 650 loop : -1.16 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 263 TYR 0.022 0.001 TYR B 328 PHE 0.019 0.002 PHE H 332 TRP 0.018 0.002 TRP G 370 HIS 0.009 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00447 (33142) covalent geometry : angle 0.61708 (45376) hydrogen bonds : bond 0.04506 ( 1055) hydrogen bonds : angle 5.12448 ( 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 363 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 271 time to evaluate : 0.969 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: 0.8254 (OUTLIER) cc_final: 0.7788 (mm) REVERT: A 193 MET cc_start: 0.3594 (tpp) cc_final: 0.2758 (tpt) REVERT: A 287 MET cc_start: 0.6157 (mmm) cc_final: 0.5638 (mmm) REVERT: A 393 LEU cc_start: 0.8212 (tp) cc_final: 0.7852 (tp) REVERT: B 355 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7426 (mtmm) REVERT: B 356 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 403 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.4000 (m-10) REVERT: C 57 THR cc_start: 0.8545 (m) cc_final: 0.8280 (m) REVERT: E 40 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8570 (mtmt) REVERT: E 72 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6087 (mtt-85) REVERT: E 364 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8166 (ptp-170) REVERT: E 476 GLU cc_start: 0.8482 (tt0) cc_final: 0.8202 (tt0) REVERT: E 484 ASP cc_start: 0.8160 (t70) cc_final: 0.7635 (t0) REVERT: F 46 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.6426 (t60) REVERT: F 190 TYR cc_start: 0.7263 (m-80) cc_final: 0.6603 (m-80) REVERT: F 193 MET cc_start: 0.1785 (tpp) cc_final: 0.0970 (tpp) REVERT: F 229 LYS cc_start: 0.5994 (ttmt) cc_final: 0.5403 (mmmt) REVERT: F 309 MET cc_start: 0.6770 (tmm) cc_final: 0.6567 (tmm) REVERT: F 323 ILE cc_start: 0.8907 (pt) cc_final: 0.8611 (mt) REVERT: F 406 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6366 (tm-30) REVERT: G 1 MET cc_start: 0.5757 (mmp) cc_final: 0.5329 (mmm) REVERT: G 107 ASN cc_start: 0.6883 (t0) cc_final: 0.6394 (t0) REVERT: G 148 TYR cc_start: 0.8060 (t80) cc_final: 0.7169 (t80) REVERT: H 254 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7169 (m-40) REVERT: H 308 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6304 (t) REVERT: H 320 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6578 (m90) REVERT: H 395 MET cc_start: 0.7181 (mmp) cc_final: 0.6930 (mmp) REVERT: M 161 MET cc_start: 0.4406 (OUTLIER) cc_final: 0.3573 (ptm) REVERT: M 273 ASP cc_start: 0.8297 (m-30) cc_final: 0.7655 (p0) outliers start: 92 outliers final: 64 residues processed: 335 average time/residue: 0.1634 time to fit residues: 92.7917 Evaluate side-chains 328 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 340 HIS 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 229 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 405 ILE 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 113 VAL Chi-restraints excluded: chain C residue 164 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 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 72 ARG 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 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 172 ASP 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 221 THR Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 405 ILE 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 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 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 161 MET Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 278 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 342 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 321 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 371 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 302 GLN E 446 ASN F 413 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.114622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.091872 restraints weight = 87045.850| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.22 r_work: 0.3471 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33142 Z= 0.136 Angle : 0.582 12.922 45376 Z= 0.303 Chirality : 0.042 0.211 4984 Planarity : 0.005 0.068 5238 Dihedral : 17.542 174.260 5960 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.15 % Favored : 94.68 % Rotamer: Outliers : 2.50 % Allowed : 16.30 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.14), residues: 3532 helix: 1.14 (0.15), residues: 1206 sheet: -1.02 (0.20), residues: 648 loop : -1.13 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 263 TYR 0.014 0.001 TYR B 56 PHE 0.017 0.001 PHE A 198 TRP 0.018 0.001 TRP E 370 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00311 (33142) covalent geometry : angle 0.58207 (45376) hydrogen bonds : bond 0.03993 ( 1055) hydrogen bonds : angle 5.00912 ( 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 364 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 284 time to evaluate : 0.903 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: 0.8262 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 193 MET cc_start: 0.3767 (tpp) cc_final: 0.2992 (tpt) REVERT: A 287 MET cc_start: 0.6157 (mmm) cc_final: 0.5709 (mmm) REVERT: A 393 LEU cc_start: 0.8049 (tp) cc_final: 0.7717 (tp) REVERT: B 356 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 403 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.4088 (m-10) REVERT: C 57 THR cc_start: 0.8460 (m) cc_final: 0.8097 (m) REVERT: C 185 LEU cc_start: 0.9019 (tp) cc_final: 0.8739 (tp) REVERT: E 40 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8568 (mtmt) REVERT: E 72 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6129 (mtt-85) REVERT: E 104 PHE cc_start: 0.6213 (m-80) cc_final: 0.6006 (t80) REVERT: E 106 TYR cc_start: 0.6676 (m-10) cc_final: 0.6153 (m-10) REVERT: E 364 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8187 (ptp-170) REVERT: E 476 GLU cc_start: 0.8448 (tt0) cc_final: 0.8158 (tt0) REVERT: E 484 ASP cc_start: 0.8117 (t70) cc_final: 0.7580 (t0) REVERT: F 46 TRP cc_start: 0.6953 (OUTLIER) cc_final: 0.6423 (t60) REVERT: F 136 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: F 190 TYR cc_start: 0.6973 (m-80) cc_final: 0.6607 (m-10) REVERT: F 193 MET cc_start: 0.2490 (tpp) cc_final: 0.1867 (tpp) REVERT: F 229 LYS cc_start: 0.5977 (ttmt) cc_final: 0.5416 (mmmt) REVERT: F 308 THR cc_start: 0.7065 (m) cc_final: 0.6802 (p) REVERT: F 309 MET cc_start: 0.6787 (tmm) cc_final: 0.6468 (tmm) REVERT: F 323 ILE cc_start: 0.8837 (pt) cc_final: 0.8584 (mt) REVERT: F 406 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6270 (tm-30) REVERT: G 1 MET cc_start: 0.5763 (mmp) cc_final: 0.5254 (mmm) REVERT: G 107 ASN cc_start: 0.6874 (t0) cc_final: 0.6391 (t0) REVERT: G 133 ASP cc_start: 0.8623 (p0) cc_final: 0.8246 (m-30) REVERT: G 148 TYR cc_start: 0.8025 (t80) cc_final: 0.7135 (t80) REVERT: G 243 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7589 (ttm110) REVERT: H 254 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7143 (m110) REVERT: H 308 THR cc_start: 0.6647 (OUTLIER) cc_final: 0.6419 (t) REVERT: H 320 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6502 (m90) REVERT: H 395 MET cc_start: 0.7019 (mmp) cc_final: 0.6766 (mmp) REVERT: M 273 ASP cc_start: 0.8282 (m-30) cc_final: 0.7688 (p0) outliers start: 80 outliers final: 57 residues processed: 339 average time/residue: 0.1641 time to fit residues: 94.4988 Evaluate side-chains 327 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 122 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 340 HIS 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 311 THR Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 405 ILE 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 113 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP 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 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 172 ASP 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 221 THR Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 405 ILE 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 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 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 223 ILE Chi-restraints excluded: chain M residue 344 GLN 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: 0.9990 chunk 249 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 259 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 302 GLN E 446 ASN G 59 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.113849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.091089 restraints weight = 87665.928| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.22 r_work: 0.3457 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33142 Z= 0.161 Angle : 0.600 13.240 45376 Z= 0.311 Chirality : 0.042 0.295 4984 Planarity : 0.005 0.068 5238 Dihedral : 17.508 173.837 5960 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 2.41 % Allowed : 16.86 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3532 helix: 1.13 (0.15), residues: 1200 sheet: -1.04 (0.21), residues: 648 loop : -1.14 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 263 TYR 0.017 0.001 TYR H 330 PHE 0.029 0.002 PHE B 358 TRP 0.019 0.001 TRP M 421 HIS 0.007 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00373 (33142) covalent geometry : angle 0.59997 (45376) hydrogen bonds : bond 0.04167 ( 1055) hydrogen bonds : angle 5.05734 ( 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 342 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 265 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7917 (mm) REVERT: A 193 MET cc_start: 0.3947 (tpp) cc_final: 0.3109 (tpp) REVERT: A 287 MET cc_start: 0.5971 (mmm) cc_final: 0.5394 (mmm) REVERT: A 393 LEU cc_start: 0.8010 (tp) cc_final: 0.7648 (tp) REVERT: B 356 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 403 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.4085 (m-10) REVERT: C 57 THR cc_start: 0.8454 (m) cc_final: 0.8186 (m) REVERT: E 40 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8569 (mtmt) REVERT: E 72 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6082 (mtt-85) REVERT: E 104 PHE cc_start: 0.6252 (m-80) cc_final: 0.5982 (t80) REVERT: E 106 TYR cc_start: 0.6773 (m-10) cc_final: 0.6251 (m-10) REVERT: E 364 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8161 (ptp-170) REVERT: E 476 GLU cc_start: 0.8461 (tt0) cc_final: 0.8186 (tt0) REVERT: E 484 ASP cc_start: 0.8216 (t70) cc_final: 0.7692 (t0) REVERT: F 46 TRP cc_start: 0.6975 (OUTLIER) cc_final: 0.6405 (t60) REVERT: F 136 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: F 190 TYR cc_start: 0.7000 (m-80) cc_final: 0.6390 (m-80) REVERT: F 193 MET cc_start: 0.2526 (tpp) cc_final: 0.1518 (tpp) REVERT: F 229 LYS cc_start: 0.6012 (ttmt) cc_final: 0.5448 (mmmt) REVERT: F 308 THR cc_start: 0.7063 (m) cc_final: 0.6813 (p) REVERT: F 309 MET cc_start: 0.6922 (tmm) cc_final: 0.6585 (tmm) REVERT: F 323 ILE cc_start: 0.8917 (pt) cc_final: 0.8666 (mt) REVERT: F 406 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6315 (tm-30) REVERT: G 1 MET cc_start: 0.5779 (mmp) cc_final: 0.5262 (mmm) REVERT: G 107 ASN cc_start: 0.6898 (t0) cc_final: 0.6422 (t0) REVERT: G 148 TYR cc_start: 0.8040 (t80) cc_final: 0.7118 (t80) REVERT: G 243 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7608 (ttm110) REVERT: H 254 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7133 (m110) REVERT: H 308 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6396 (t) REVERT: H 320 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6563 (m90) REVERT: H 395 MET cc_start: 0.7193 (mmp) cc_final: 0.6980 (mmp) REVERT: M 273 ASP cc_start: 0.8207 (m-30) cc_final: 0.7645 (p0) outliers start: 77 outliers final: 58 residues processed: 318 average time/residue: 0.1720 time to fit residues: 92.1110 Evaluate side-chains 325 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 122 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 340 HIS 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 311 THR Chi-restraints excluded: chain B residue 403 TYR 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 113 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP 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 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 136 GLU 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 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 221 THR Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 405 ILE 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 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 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 57 LEU Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 344 GLN 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: 0.0170 chunk 291 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS B 439 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN G 205 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.114556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091136 restraints weight = 88741.811| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.33 r_work: 0.3456 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33142 Z= 0.152 Angle : 0.597 13.363 45376 Z= 0.309 Chirality : 0.042 0.205 4984 Planarity : 0.005 0.080 5238 Dihedral : 17.480 173.203 5960 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.41 % Favored : 94.39 % Rotamer: Outliers : 2.35 % Allowed : 17.18 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3532 helix: 1.13 (0.15), residues: 1208 sheet: -1.03 (0.21), residues: 648 loop : -1.16 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 263 TYR 0.034 0.001 TYR C 190 PHE 0.027 0.001 PHE B 358 TRP 0.032 0.001 TRP M 421 HIS 0.007 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00351 (33142) covalent geometry : angle 0.59656 (45376) hydrogen bonds : bond 0.04070 ( 1055) hydrogen bonds : angle 5.03376 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6440.89 seconds wall clock time: 111 minutes 48.99 seconds (6708.99 seconds total)