Starting phenix.real_space_refine on Fri May 30 05:49:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozg_17308/05_2025/8ozg_17308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozg_17308/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozg_17308/05_2025/8ozg_17308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozg_17308/05_2025/8ozg_17308.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozg_17308/05_2025/8ozg_17308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozg_17308/05_2025/8ozg_17308.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.53, per 1000 atoms: 0.61 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: 7.80 Conformation dependent library (CDL) restraints added in 3.8 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 26 sheets defined 40.0% alpha, 14.9% beta 21 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 10.64 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: 11.63 Time building geometry restraints manager: 9.13 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 75.790 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.950 ------------------------------------------------------------------------------- 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 : 12.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (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 TRP 0.032 0.002 TRP M 320 HIS 0.005 0.001 HIS G 59 PHE 0.025 0.002 PHE C 343 TYR 0.016 0.001 TYR G 56 ARG 0.005 0.000 ARG F 240 Details of bonding type rmsd hydrogen bonds : bond 0.18812 ( 1055) hydrogen bonds : angle 7.36024 ( 2877) covalent geometry : bond 0.00600 (33142) covalent geometry : angle 0.72669 (45376) *********************** 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 : 3.342 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: 0.7364 (tp30) REVERT: E 40 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8011 (mtmt) REVERT: E 484 ASP cc_start: 0.7989 (t70) cc_final: 0.7521 (t0) REVERT: F 192 TRP cc_start: 0.6056 (p-90) cc_final: 0.5636 (p-90) REVERT: F 317 LYS cc_start: 0.5364 (mttm) cc_final: 0.5135 (mtmm) 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: 0.4631 (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: 0.6959 (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: 0.4075 time to fit residues: 284.5779 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 : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 184 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 326 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** C 9 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 302 GLN G 329 HIS ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 HIS M 360 HIS M 430 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.115851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.092509 restraints weight = 87540.892| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.30 r_work: 0.3479 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33142 Z= 0.224 Angle : 0.678 11.298 45376 Z= 0.358 Chirality : 0.045 0.312 4984 Planarity : 0.005 0.103 5238 Dihedral : 17.732 179.693 5960 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 1.44 % Allowed : 8.17 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3532 helix: 0.80 (0.15), residues: 1206 sheet: -1.01 (0.21), residues: 630 loop : -1.26 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 370 HIS 0.009 0.001 HIS A 160 PHE 0.033 0.002 PHE A 17 TYR 0.023 0.002 TYR G 280 ARG 0.005 0.001 ARG M 152 Details of bonding type rmsd hydrogen bonds : bond 0.05351 ( 1055) hydrogen bonds : angle 5.53198 ( 2877) covalent geometry : bond 0.00510 (33142) covalent geometry : angle 0.67824 (45376) *********************** 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 369 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 3.722 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: A 287 MET cc_start: 0.6014 (mmm) cc_final: 0.5647 (mmm) REVERT: A 395 MET cc_start: 0.6108 (tpp) cc_final: 0.5664 (mtp) REVERT: A 401 VAL cc_start: 0.7810 (t) cc_final: 0.6741 (t) REVERT: B 74 MET cc_start: 0.8519 (ppp) cc_final: 0.8057 (ppp) REVERT: B 85 LYS cc_start: 0.8853 (mttt) cc_final: 0.8441 (mtmt) REVERT: B 364 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7017 (mtt180) REVERT: E 40 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8340 (mtmt) REVERT: E 106 TYR cc_start: 0.7469 (m-10) cc_final: 0.7260 (m-10) REVERT: E 116 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8318 (t0) REVERT: E 446 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8724 (t160) REVERT: E 476 GLU cc_start: 0.8443 (tt0) cc_final: 0.8103 (tt0) REVERT: E 484 ASP cc_start: 0.8356 (t70) cc_final: 0.7804 (t0) REVERT: F 190 TYR cc_start: 0.7548 (m-80) cc_final: 0.6794 (m-10) REVERT: F 192 TRP cc_start: 0.5787 (p-90) cc_final: 0.5465 (p-90) REVERT: F 217 PHE cc_start: 0.7335 (m-80) cc_final: 0.7130 (m-80) REVERT: F 221 TYR cc_start: 0.6989 (m-80) cc_final: 0.6642 (m-80) REVERT: F 277 MET cc_start: 0.6946 (mmt) cc_final: 0.6675 (mmm) REVERT: F 317 LYS cc_start: 0.5597 (mttm) cc_final: 0.5248 (mtmm) REVERT: F 406 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6255 (tm-30) REVERT: G 107 ASN cc_start: 0.6906 (t0) cc_final: 0.6400 (t0) REVERT: H 133 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8786 (mt-10) REVERT: H 193 MET cc_start: 0.6220 (ttm) cc_final: 0.5914 (mmm) REVERT: H 308 THR cc_start: 0.6171 (OUTLIER) cc_final: 0.5914 (t) REVERT: H 381 ILE cc_start: 0.7611 (mt) cc_final: 0.7175 (pt) REVERT: M 245 PHE cc_start: 0.7385 (m-10) cc_final: 0.7074 (m-10) REVERT: M 406 LEU cc_start: 0.9159 (mm) cc_final: 0.8922 (mm) outliers start: 46 outliers final: 31 residues processed: 351 average time/residue: 0.4000 time to fit residues: 233.9427 Evaluate side-chains 309 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 3.539 ------------------------------------------------------------------------------- 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 116 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 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 G residue 426 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 199 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN H 156 GLN M 61 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 = 0.3967 r_free = 0.3967 target = 0.112680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089444 restraints weight = 88410.667| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.27 r_work: 0.3421 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 33142 Z= 0.260 Angle : 0.688 10.336 45376 Z= 0.364 Chirality : 0.045 0.315 4984 Planarity : 0.006 0.087 5238 Dihedral : 17.886 178.945 5960 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer: Outliers : 2.41 % Allowed : 10.98 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3532 helix: 0.68 (0.15), residues: 1196 sheet: -1.10 (0.22), residues: 568 loop : -1.25 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 370 HIS 0.008 0.002 HIS C 188 PHE 0.027 0.002 PHE A 198 TYR 0.024 0.002 TYR M 280 ARG 0.005 0.001 ARG C 240 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 1055) hydrogen bonds : angle 5.43736 ( 2877) covalent geometry : bond 0.00593 (33142) covalent geometry : angle 0.68805 (45376) *********************** 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 365 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 3.491 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: 0.8521 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 393 LEU cc_start: 0.8156 (tp) cc_final: 0.7380 (tp) REVERT: A 401 VAL cc_start: 0.7823 (t) cc_final: 0.6547 (t) REVERT: B 74 MET cc_start: 0.8585 (ppp) cc_final: 0.8087 (ppp) REVERT: B 85 LYS cc_start: 0.9065 (mttt) cc_final: 0.8828 (mttp) REVERT: C 309 MET cc_start: 0.6822 (ptm) cc_final: 0.6579 (ptm) REVERT: E 40 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8467 (mtmt) REVERT: E 476 GLU cc_start: 0.8412 (tt0) cc_final: 0.8063 (tt0) REVERT: E 484 ASP cc_start: 0.8390 (t70) cc_final: 0.7813 (t0) REVERT: F 130 ASP cc_start: 0.8983 (m-30) cc_final: 0.8727 (m-30) REVERT: F 190 TYR cc_start: 0.7414 (m-80) cc_final: 0.6892 (m-10) REVERT: F 217 PHE cc_start: 0.7227 (m-80) cc_final: 0.6902 (m-80) REVERT: F 406 GLU cc_start: 0.6411 (tm-30) cc_final: 0.6100 (tm-30) REVERT: G 1 MET cc_start: 0.5951 (mmp) cc_final: 0.5245 (mmt) REVERT: G 107 ASN cc_start: 0.6946 (t0) cc_final: 0.6490 (t0) REVERT: G 348 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: G 399 THR cc_start: 0.6131 (OUTLIER) cc_final: 0.5903 (p) REVERT: H 308 THR cc_start: 0.6645 (OUTLIER) cc_final: 0.6423 (t) REVERT: H 320 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6750 (m90) REVERT: H 381 ILE cc_start: 0.7613 (mt) cc_final: 0.7138 (pt) REVERT: M 245 PHE cc_start: 0.7685 (m-10) cc_final: 0.7444 (m-10) outliers start: 77 outliers final: 46 residues processed: 336 average time/residue: 0.3872 time to fit residues: 220.6488 Evaluate side-chains 297 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 GLN 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 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain 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 399 THR Chi-restraints excluded: chain G residue 501 LEU 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 200 TYR 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 41 optimal weight: 8.9990 chunk 329 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 156 GLN C 270 ASN ** E 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.114328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.090930 restraints weight = 88821.518| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.29 r_work: 0.3458 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33142 Z= 0.186 Angle : 0.613 9.344 45376 Z= 0.325 Chirality : 0.043 0.263 4984 Planarity : 0.005 0.082 5238 Dihedral : 17.807 178.312 5960 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 2.44 % Allowed : 12.83 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3532 helix: 0.87 (0.15), residues: 1184 sheet: -1.00 (0.21), residues: 602 loop : -1.25 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 370 HIS 0.009 0.001 HIS C 188 PHE 0.024 0.002 PHE A 198 TYR 0.025 0.001 TYR C 190 ARG 0.004 0.000 ARG H 126 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1055) hydrogen bonds : angle 5.20069 ( 2877) covalent geometry : bond 0.00424 (33142) covalent geometry : angle 0.61261 (45376) *********************** 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: 78 poor density : 291 time to evaluate : 3.604 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 40 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.5258 (p0) REVERT: A 87 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 88 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7871 (mm) REVERT: B 74 MET cc_start: 0.8498 (ppp) cc_final: 0.8042 (ppp) REVERT: B 356 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 40 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8516 (mtmt) REVERT: E 476 GLU cc_start: 0.8386 (tt0) cc_final: 0.8101 (tt0) REVERT: E 484 ASP cc_start: 0.8396 (t70) cc_final: 0.7815 (t0) REVERT: F 190 TYR cc_start: 0.7360 (m-80) cc_final: 0.6820 (m-80) REVERT: F 217 PHE cc_start: 0.7342 (m-80) cc_final: 0.7026 (m-80) REVERT: F 406 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6255 (tm-30) REVERT: G 1 MET cc_start: 0.5869 (mmp) cc_final: 0.5086 (mmm) REVERT: G 107 ASN cc_start: 0.6882 (t0) cc_final: 0.6446 (t0) REVERT: G 148 TYR cc_start: 0.8046 (t80) cc_final: 0.7160 (t80) REVERT: G 348 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: G 399 THR cc_start: 0.6136 (OUTLIER) cc_final: 0.5847 (p) REVERT: H 308 THR cc_start: 0.6502 (OUTLIER) cc_final: 0.6205 (t) REVERT: H 320 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6801 (m90) REVERT: H 381 ILE cc_start: 0.7696 (mt) cc_final: 0.7335 (pt) REVERT: M 150 TYR cc_start: 0.8559 (m-80) cc_final: 0.8311 (m-10) REVERT: M 245 PHE cc_start: 0.7716 (m-10) cc_final: 0.7491 (m-10) outliers start: 78 outliers final: 49 residues processed: 348 average time/residue: 0.3876 time to fit residues: 226.4231 Evaluate side-chains 319 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 3.504 ------------------------------------------------------------------------------- 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 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 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 131 ILE 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 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 F residue 164 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 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 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 405 ILE 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 273 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 237 optimal weight: 7.9990 chunk 48 optimal weight: 0.0060 chunk 88 optimal weight: 10.0000 chunk 343 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 258 optimal weight: 2.9990 chunk 201 optimal weight: 0.2980 chunk 125 optimal weight: 7.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN 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** H 174 ASN H 357 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.115594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092751 restraints weight = 86859.937| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.22 r_work: 0.3487 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33142 Z= 0.127 Angle : 0.571 9.832 45376 Z= 0.301 Chirality : 0.042 0.232 4984 Planarity : 0.005 0.076 5238 Dihedral : 17.655 177.181 5960 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.87 % Favored : 94.90 % Rotamer: Outliers : 2.50 % Allowed : 14.21 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3532 helix: 1.04 (0.15), residues: 1206 sheet: -0.82 (0.21), residues: 622 loop : -1.18 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 370 HIS 0.009 0.001 HIS G 59 PHE 0.022 0.001 PHE A 198 TYR 0.016 0.001 TYR C 190 ARG 0.004 0.000 ARG H 126 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1055) hydrogen bonds : angle 5.00190 ( 2877) covalent geometry : bond 0.00285 (33142) covalent geometry : angle 0.57085 (45376) *********************** 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 395 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 315 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.5796 (mmm) cc_final: 0.5470 (mmm) REVERT: A 314 GLN cc_start: 0.5340 (tt0) cc_final: 0.4915 (tm-30) REVERT: A 393 LEU cc_start: 0.8305 (tp) cc_final: 0.7763 (tp) REVERT: B 356 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 57 THR cc_start: 0.8432 (m) cc_final: 0.8175 (m) REVERT: E 40 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8542 (mtmt) REVERT: E 476 GLU cc_start: 0.8434 (tt0) cc_final: 0.8107 (tt0) REVERT: E 484 ASP cc_start: 0.8179 (t70) cc_final: 0.7658 (t0) REVERT: F 15 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7626 (p0) REVERT: F 190 TYR cc_start: 0.7327 (m-80) cc_final: 0.7046 (m-80) REVERT: F 217 PHE cc_start: 0.7356 (m-80) cc_final: 0.6785 (m-80) REVERT: F 406 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6383 (tm-30) REVERT: G 1 MET cc_start: 0.5696 (mmp) cc_final: 0.5354 (mmm) REVERT: G 107 ASN cc_start: 0.6878 (t0) cc_final: 0.6433 (t0) REVERT: G 222 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: G 399 THR cc_start: 0.6093 (OUTLIER) cc_final: 0.5824 (p) REVERT: H 212 ASN cc_start: 0.7595 (p0) cc_final: 0.7134 (p0) REVERT: H 254 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7356 (m-40) REVERT: H 308 THR cc_start: 0.6585 (OUTLIER) cc_final: 0.6310 (t) REVERT: H 320 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6637 (m90) REVERT: H 336 MET cc_start: 0.8224 (mtm) cc_final: 0.7846 (mpp) REVERT: H 381 ILE cc_start: 0.7657 (mt) cc_final: 0.7289 (pt) REVERT: M 150 TYR cc_start: 0.8645 (m-80) cc_final: 0.8381 (m-10) REVERT: M 245 PHE cc_start: 0.7614 (m-10) cc_final: 0.7406 (m-10) outliers start: 80 outliers final: 42 residues processed: 371 average time/residue: 0.3922 time to fit residues: 242.8552 Evaluate side-chains 315 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 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 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 222 GLN Chi-restraints excluded: chain G residue 399 THR 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 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 170 ILE Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 297 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 283 optimal weight: 0.2980 chunk 251 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 135 optimal weight: 0.3980 chunk 305 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4019 r_free = 0.4019 target = 0.115439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.092562 restraints weight = 87666.710| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.24 r_work: 0.3485 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33142 Z= 0.135 Angle : 0.574 11.410 45376 Z= 0.301 Chirality : 0.042 0.218 4984 Planarity : 0.005 0.072 5238 Dihedral : 17.583 176.649 5960 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 2.75 % Allowed : 14.71 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3532 helix: 1.06 (0.15), residues: 1208 sheet: -0.89 (0.21), residues: 638 loop : -1.18 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 370 HIS 0.009 0.001 HIS G 59 PHE 0.024 0.001 PHE H 332 TYR 0.014 0.001 TYR C 190 ARG 0.007 0.000 ARG H 263 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1055) hydrogen bonds : angle 4.96526 ( 2877) covalent geometry : bond 0.00309 (33142) covalent geometry : angle 0.57445 (45376) *********************** 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 365 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 277 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7752 (mm) REVERT: A 393 LEU cc_start: 0.8251 (tp) cc_final: 0.7773 (tp) REVERT: B 356 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 403 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.4259 (m-10) REVERT: C 37 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8783 (tt) REVERT: C 57 THR cc_start: 0.8472 (m) cc_final: 0.8242 (m) REVERT: C 122 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7103 (ppp) REVERT: E 40 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8547 (mtmt) REVERT: E 72 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.6032 (mtt-85) REVERT: E 104 PHE cc_start: 0.6518 (m-80) cc_final: 0.6301 (t80) REVERT: E 116 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8236 (t70) REVERT: E 433 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5006 (pp) REVERT: E 476 GLU cc_start: 0.8440 (tt0) cc_final: 0.8142 (tt0) REVERT: E 484 ASP cc_start: 0.8161 (t70) cc_final: 0.7642 (t0) REVERT: F 15 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (p0) REVERT: F 46 TRP cc_start: 0.7178 (OUTLIER) cc_final: 0.6523 (t60) REVERT: F 130 ASP cc_start: 0.8916 (m-30) cc_final: 0.8699 (m-30) REVERT: F 190 TYR cc_start: 0.7312 (m-80) cc_final: 0.7016 (m-80) REVERT: F 395 MET cc_start: 0.5084 (tpt) cc_final: 0.4317 (tpt) REVERT: F 406 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6507 (tm-30) REVERT: G 1 MET cc_start: 0.5681 (mmp) cc_final: 0.5304 (mmm) REVERT: G 74 MET cc_start: 0.7766 (tmm) cc_final: 0.7500 (tmm) REVERT: G 107 ASN cc_start: 0.6809 (t0) cc_final: 0.6313 (t0) REVERT: G 399 THR cc_start: 0.6222 (OUTLIER) cc_final: 0.5928 (p) REVERT: H 212 ASN cc_start: 0.7642 (p0) cc_final: 0.7186 (p0) REVERT: H 254 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: H 308 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6211 (t) REVERT: H 320 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6598 (m90) REVERT: H 336 MET cc_start: 0.8223 (mtm) cc_final: 0.7776 (mpp) REVERT: H 381 ILE cc_start: 0.7734 (mt) cc_final: 0.7358 (pt) REVERT: M 273 ASP cc_start: 0.8178 (m-30) cc_final: 0.7572 (p0) outliers start: 88 outliers final: 53 residues processed: 338 average time/residue: 0.3762 time to fit residues: 216.6907 Evaluate side-chains 325 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 3.732 ------------------------------------------------------------------------------- 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 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 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 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 122 MET 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 60 ILE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 46 TRP 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 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 399 THR 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 170 ILE 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 57 LEU Chi-restraints excluded: chain M residue 223 ILE 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 64 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 353 optimal weight: 0.9980 chunk 138 optimal weight: 0.1980 chunk 319 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 52 optimal weight: 8.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 302 GLN E 446 ASN G 205 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.116617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093752 restraints weight = 87290.174| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.24 r_work: 0.3507 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33142 Z= 0.117 Angle : 0.560 12.075 45376 Z= 0.292 Chirality : 0.041 0.208 4984 Planarity : 0.004 0.068 5238 Dihedral : 17.470 174.935 5960 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.98 % Favored : 94.79 % Rotamer: Outliers : 2.47 % Allowed : 15.08 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3532 helix: 1.21 (0.15), residues: 1206 sheet: -0.76 (0.21), residues: 642 loop : -1.13 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 219 HIS 0.009 0.001 HIS G 59 PHE 0.018 0.001 PHE A 198 TYR 0.016 0.001 TYR H 330 ARG 0.006 0.000 ARG H 263 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1055) hydrogen bonds : angle 4.88279 ( 2877) covalent geometry : bond 0.00261 (33142) covalent geometry : angle 0.56048 (45376) *********************** 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 370 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 291 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7807 (mm) REVERT: A 193 MET cc_start: 0.4026 (ttm) cc_final: 0.3539 (tpt) REVERT: A 287 MET cc_start: 0.5757 (mmm) cc_final: 0.5020 (tpt) REVERT: A 393 LEU cc_start: 0.8007 (tp) cc_final: 0.7791 (tp) REVERT: A 395 MET cc_start: 0.4245 (pmm) cc_final: 0.3715 (pmm) REVERT: B 403 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.4321 (m-10) REVERT: C 37 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8830 (tt) REVERT: C 57 THR cc_start: 0.8452 (m) cc_final: 0.8217 (m) REVERT: C 122 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.7045 (ppp) REVERT: E 72 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.6142 (mtt-85) REVERT: E 106 TYR cc_start: 0.6710 (m-10) cc_final: 0.6169 (m-10) REVERT: E 116 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8175 (t0) REVERT: E 433 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.4867 (pp) REVERT: E 476 GLU cc_start: 0.8408 (tt0) cc_final: 0.8101 (tt0) REVERT: E 484 ASP cc_start: 0.8130 (t70) cc_final: 0.7639 (t0) REVERT: F 46 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.6407 (t60) REVERT: F 190 TYR cc_start: 0.7289 (m-80) cc_final: 0.6954 (m-80) REVERT: F 308 THR cc_start: 0.7090 (m) cc_final: 0.6730 (p) REVERT: F 309 MET cc_start: 0.6740 (tmm) cc_final: 0.6530 (tmm) REVERT: F 406 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6515 (tm-30) REVERT: G 1 MET cc_start: 0.5626 (mmp) cc_final: 0.5139 (mmm) REVERT: G 107 ASN cc_start: 0.6812 (t0) cc_final: 0.6313 (t0) REVERT: G 133 ASP cc_start: 0.8533 (p0) cc_final: 0.8211 (m-30) REVERT: G 303 MET cc_start: 0.8588 (ttp) cc_final: 0.8350 (ptt) REVERT: G 399 THR cc_start: 0.6168 (OUTLIER) cc_final: 0.5909 (p) REVERT: H 212 ASN cc_start: 0.7701 (p0) cc_final: 0.7243 (p0) REVERT: H 254 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7308 (m-40) REVERT: H 308 THR cc_start: 0.6085 (OUTLIER) cc_final: 0.5766 (t) REVERT: H 320 HIS cc_start: 0.6957 (m-70) cc_final: 0.6562 (m90) REVERT: H 336 MET cc_start: 0.8122 (mtm) cc_final: 0.7793 (mpp) REVERT: H 381 ILE cc_start: 0.7601 (mt) cc_final: 0.7200 (pt) REVERT: M 273 ASP cc_start: 0.8246 (m-30) cc_final: 0.7626 (p0) outliers start: 79 outliers final: 54 residues processed: 340 average time/residue: 0.3831 time to fit residues: 221.9018 Evaluate side-chains 322 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 351 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 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 C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 122 MET 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 60 ILE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain 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 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 399 THR 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 94 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 202 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 82 optimal weight: 0.0010 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 166 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 overall best weight: 2.0590 ------------------------------------------------------------------------------- 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** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 302 GLN 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 = 0.4013 r_free = 0.4013 target = 0.115073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092159 restraints weight = 87842.021| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.23 r_work: 0.3480 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33142 Z= 0.153 Angle : 0.585 10.303 45376 Z= 0.306 Chirality : 0.042 0.249 4984 Planarity : 0.005 0.068 5238 Dihedral : 17.442 175.085 5960 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.41 % Favored : 94.39 % Rotamer: Outliers : 2.91 % Allowed : 15.33 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3532 helix: 1.20 (0.15), residues: 1208 sheet: -0.76 (0.21), residues: 632 loop : -1.14 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 219 HIS 0.009 0.001 HIS G 59 PHE 0.031 0.001 PHE B 358 TYR 0.016 0.001 TYR H 330 ARG 0.005 0.000 ARG H 263 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 1055) hydrogen bonds : angle 4.92962 ( 2877) covalent geometry : bond 0.00350 (33142) covalent geometry : angle 0.58537 (45376) *********************** 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 360 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 267 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 393 LEU cc_start: 0.7995 (tp) cc_final: 0.7726 (tp) REVERT: B 148 TYR cc_start: 0.6166 (t80) cc_final: 0.5922 (t80) REVERT: B 358 PHE cc_start: 0.8161 (m-80) cc_final: 0.7786 (m-80) REVERT: B 403 TYR cc_start: 0.5908 (OUTLIER) cc_final: 0.4191 (m-10) REVERT: C 57 THR cc_start: 0.8465 (m) cc_final: 0.8220 (m) REVERT: C 266 VAL cc_start: 0.8912 (t) cc_final: 0.8708 (m) REVERT: E 54 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8592 (ptp-110) REVERT: E 72 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6276 (mtt-85) REVERT: E 104 PHE cc_start: 0.6509 (m-80) cc_final: 0.6195 (t80) REVERT: E 106 TYR cc_start: 0.6756 (m-10) cc_final: 0.6252 (m-10) REVERT: E 116 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8318 (t70) REVERT: E 476 GLU cc_start: 0.8449 (tt0) cc_final: 0.8153 (tt0) REVERT: E 484 ASP cc_start: 0.8204 (t70) cc_final: 0.7684 (t0) REVERT: F 15 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7541 (p0) REVERT: F 46 TRP cc_start: 0.7073 (OUTLIER) cc_final: 0.6418 (t60) REVERT: F 136 GLU cc_start: 0.8564 (mp0) cc_final: 0.8260 (mp0) REVERT: F 190 TYR cc_start: 0.7270 (m-80) cc_final: 0.6614 (m-80) REVERT: F 193 MET cc_start: 0.1848 (tpp) cc_final: 0.1191 (tpp) REVERT: F 229 LYS cc_start: 0.5827 (ttmt) cc_final: 0.5187 (mmmt) REVERT: F 309 MET cc_start: 0.6647 (tmm) cc_final: 0.6437 (tmm) REVERT: F 406 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6427 (tm-30) REVERT: G 1 MET cc_start: 0.5659 (mmp) cc_final: 0.5163 (mmm) REVERT: G 107 ASN cc_start: 0.6864 (t0) cc_final: 0.6355 (t0) REVERT: G 399 THR cc_start: 0.6315 (OUTLIER) cc_final: 0.6051 (p) REVERT: H 212 ASN cc_start: 0.7724 (p0) cc_final: 0.7279 (p0) REVERT: H 254 ASN cc_start: 0.8201 (t0) cc_final: 0.7217 (m-40) REVERT: H 277 MET cc_start: 0.8510 (mmm) cc_final: 0.8191 (mmm) REVERT: H 308 THR cc_start: 0.6166 (OUTLIER) cc_final: 0.5846 (t) REVERT: H 320 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6620 (m90) REVERT: H 381 ILE cc_start: 0.7589 (mt) cc_final: 0.7194 (pt) REVERT: M 273 ASP cc_start: 0.8273 (m-30) cc_final: 0.7634 (p0) outliers start: 93 outliers final: 65 residues processed: 330 average time/residue: 0.3824 time to fit residues: 214.4368 Evaluate side-chains 331 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 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 403 TYR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 470 CYS 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 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 116 ASP 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 46 TRP 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 399 THR 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 170 ILE 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 H residue 384 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 252 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 327 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 226 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.113600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.090843 restraints weight = 87850.110| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.21 r_work: 0.3452 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33142 Z= 0.186 Angle : 0.614 9.864 45376 Z= 0.320 Chirality : 0.043 0.259 4984 Planarity : 0.005 0.067 5238 Dihedral : 17.487 175.417 5960 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.52 % Favored : 94.25 % Rotamer: Outliers : 2.47 % Allowed : 16.08 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3532 helix: 1.13 (0.15), residues: 1204 sheet: -0.90 (0.21), residues: 638 loop : -1.12 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 219 HIS 0.008 0.001 HIS G 59 PHE 0.028 0.002 PHE E 104 TYR 0.018 0.001 TYR B 56 ARG 0.007 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 1055) hydrogen bonds : angle 5.02656 ( 2877) covalent geometry : bond 0.00426 (33142) covalent geometry : angle 0.61410 (45376) *********************** 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 346 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 267 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 193 MET cc_start: 0.3948 (ttm) cc_final: 0.3413 (tpt) REVERT: A 287 MET cc_start: 0.6098 (mmm) cc_final: 0.5395 (mmm) REVERT: B 13 LEU cc_start: 0.8076 (tp) cc_final: 0.7831 (tp) REVERT: B 403 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.4077 (m-10) REVERT: C 57 THR cc_start: 0.8529 (m) cc_final: 0.8280 (m) REVERT: C 266 VAL cc_start: 0.8963 (t) cc_final: 0.8729 (m) REVERT: E 72 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6170 (mtt-85) REVERT: E 104 PHE cc_start: 0.6707 (m-80) cc_final: 0.6215 (t80) REVERT: E 106 TYR cc_start: 0.6700 (m-10) cc_final: 0.6235 (m-10) REVERT: E 116 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8292 (t70) REVERT: E 476 GLU cc_start: 0.8413 (tt0) cc_final: 0.8137 (tt0) REVERT: E 484 ASP cc_start: 0.8232 (t70) cc_final: 0.7706 (t0) REVERT: F 15 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7652 (p0) REVERT: F 46 TRP cc_start: 0.6994 (OUTLIER) cc_final: 0.6447 (t60) REVERT: F 190 TYR cc_start: 0.7283 (m-80) cc_final: 0.6624 (m-80) REVERT: F 309 MET cc_start: 0.6596 (tmm) cc_final: 0.6385 (tmm) REVERT: F 406 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6639 (tm-30) REVERT: G 1 MET cc_start: 0.5600 (mmp) cc_final: 0.5136 (mmm) REVERT: G 107 ASN cc_start: 0.6878 (t0) cc_final: 0.6371 (t0) REVERT: G 148 TYR cc_start: 0.8029 (t80) cc_final: 0.7161 (t80) REVERT: G 399 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.6093 (p) REVERT: H 254 ASN cc_start: 0.8240 (t0) cc_final: 0.7166 (m-40) REVERT: H 277 MET cc_start: 0.8505 (mmm) cc_final: 0.8186 (mmm) REVERT: H 308 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.6004 (t) REVERT: H 309 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6922 (ttt) REVERT: H 320 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6594 (m90) REVERT: H 381 ILE cc_start: 0.7514 (mt) cc_final: 0.7169 (pt) REVERT: M 273 ASP cc_start: 0.8291 (m-30) cc_final: 0.7666 (p0) outliers start: 79 outliers final: 59 residues processed: 319 average time/residue: 0.3896 time to fit residues: 210.8688 Evaluate side-chains 325 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 351 ILE 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 111 HIS Chi-restraints excluded: chain B residue 147 ILE 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 470 CYS 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 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 116 ASP 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 437 VAL 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 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 399 THR 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 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 309 MET 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 228 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 160 optimal weight: 0.2980 chunk 227 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 B 439 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 302 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.115649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.092931 restraints weight = 87124.752| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.23 r_work: 0.3491 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3569 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= 0.128 Angle : 0.577 12.488 45376 Z= 0.299 Chirality : 0.042 0.243 4984 Planarity : 0.004 0.066 5238 Dihedral : 17.395 172.313 5960 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.07 % Favored : 94.73 % Rotamer: Outliers : 2.10 % Allowed : 16.74 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3532 helix: 1.19 (0.15), residues: 1216 sheet: -0.89 (0.21), residues: 648 loop : -1.12 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 219 HIS 0.008 0.001 HIS G 59 PHE 0.021 0.001 PHE H 332 TYR 0.017 0.001 TYR B 148 ARG 0.006 0.000 ARG H 263 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 1055) hydrogen bonds : angle 4.91796 ( 2877) covalent geometry : bond 0.00289 (33142) covalent geometry : angle 0.57687 (45376) ********************** 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 351 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 193 MET cc_start: 0.4087 (ttm) cc_final: 0.3840 (tpt) REVERT: A 287 MET cc_start: 0.6321 (mmm) cc_final: 0.5476 (mmm) REVERT: A 392 TYR cc_start: 0.6464 (p90) cc_final: 0.6234 (p90) REVERT: A 393 LEU cc_start: 0.7882 (tp) cc_final: 0.7410 (tp) REVERT: B 403 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.4178 (m-10) REVERT: C 57 THR cc_start: 0.8451 (m) cc_final: 0.8129 (m) REVERT: C 266 VAL cc_start: 0.8763 (t) cc_final: 0.8557 (m) REVERT: E 54 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8549 (ptp-110) REVERT: E 72 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.6033 (mtt-85) REVERT: E 104 PHE cc_start: 0.6481 (m-80) cc_final: 0.6206 (t80) REVERT: E 106 TYR cc_start: 0.6738 (m-10) cc_final: 0.6310 (m-10) REVERT: E 116 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8336 (t70) REVERT: E 476 GLU cc_start: 0.8418 (tt0) cc_final: 0.8111 (tt0) REVERT: E 484 ASP cc_start: 0.8204 (t70) cc_final: 0.7707 (t0) REVERT: F 15 ASN cc_start: 0.7769 (p0) cc_final: 0.7503 (p0) REVERT: F 46 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.6324 (t60) REVERT: F 190 TYR cc_start: 0.6892 (m-80) cc_final: 0.6399 (m-80) REVERT: F 229 LYS cc_start: 0.6101 (ttmt) cc_final: 0.5444 (mmmt) REVERT: F 309 MET cc_start: 0.6753 (tmm) cc_final: 0.6552 (tmm) REVERT: F 406 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6639 (tm-30) REVERT: G 1 MET cc_start: 0.5840 (mmp) cc_final: 0.5288 (mmm) REVERT: G 107 ASN cc_start: 0.6866 (t0) cc_final: 0.6358 (t0) REVERT: G 344 GLN cc_start: 0.8538 (mm110) cc_final: 0.8032 (mm110) REVERT: G 399 THR cc_start: 0.6342 (OUTLIER) cc_final: 0.6072 (p) REVERT: H 254 ASN cc_start: 0.8075 (t0) cc_final: 0.7151 (m110) REVERT: H 277 MET cc_start: 0.8355 (mmm) cc_final: 0.8021 (mmm) REVERT: H 308 THR cc_start: 0.6254 (OUTLIER) cc_final: 0.5922 (t) REVERT: H 309 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6980 (ttt) REVERT: H 320 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6533 (m90) REVERT: H 381 ILE cc_start: 0.7673 (mt) cc_final: 0.7299 (pt) REVERT: M 150 TYR cc_start: 0.8533 (m-80) cc_final: 0.8199 (m-80) REVERT: M 273 ASP cc_start: 0.8260 (m-30) cc_final: 0.7670 (p0) outliers start: 67 outliers final: 50 residues processed: 324 average time/residue: 0.3918 time to fit residues: 213.7509 Evaluate side-chains 317 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 3.842 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 351 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 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 470 CYS Chi-restraints excluded: chain B residue 484 ASP 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 E residue 60 ILE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 116 ASP 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 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 46 TRP 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 338 LEU Chi-restraints excluded: chain G residue 399 THR 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 94 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain H residue 384 LEU 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 65 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 187 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 302 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.112677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.089384 restraints weight = 88655.614| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.29 r_work: 0.3421 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 33142 Z= 0.241 Angle : 0.665 12.132 45376 Z= 0.345 Chirality : 0.044 0.277 4984 Planarity : 0.005 0.067 5238 Dihedral : 17.506 174.514 5960 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.34 % Favored : 93.46 % Rotamer: Outliers : 2.47 % Allowed : 16.83 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3532 helix: 1.01 (0.15), residues: 1204 sheet: -1.05 (0.21), residues: 650 loop : -1.17 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 421 HIS 0.009 0.002 HIS G 59 PHE 0.027 0.002 PHE E 104 TYR 0.023 0.002 TYR C 190 ARG 0.005 0.001 ARG H 263 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 1055) hydrogen bonds : angle 5.15603 ( 2877) covalent geometry : bond 0.00552 (33142) covalent geometry : angle 0.66451 (45376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14009.12 seconds wall clock time: 244 minutes 46.69 seconds (14686.69 seconds total)