Starting phenix.real_space_refine on Mon Nov 18 04:17:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/11_2024/8op1_17035.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/11_2024/8op1_17035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/11_2024/8op1_17035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/11_2024/8op1_17035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/11_2024/8op1_17035.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/11_2024/8op1_17035.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 80 5.16 5 C 9630 2.51 5 N 2655 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15415 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "D" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "E" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 10.70, per 1000 atoms: 0.69 Number of scatterers: 15415 At special positions: 0 Unit cell: (178.62, 117.935, 117.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 35 15.00 O 3015 8.00 N 2655 7.00 C 9630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 2.1 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 13 sheets defined 68.0% alpha, 4.8% beta 0 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 58 through 61 removed outlier: 4.168A pdb=" N PHE A 61 " --> pdb=" O ASN A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.563A pdb=" N ARG A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.097A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.764A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.825A pdb=" N GLY A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.755A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.806A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.529A pdb=" N VAL B 6 " --> pdb=" O LEU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 61 through 75 removed outlier: 4.044A pdb=" N ILE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 removed outlier: 3.535A pdb=" N GLN B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.645A pdb=" N ARG B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 231 removed outlier: 4.175A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.622A pdb=" N ASN B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.173A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.553A pdb=" N LEU B 272 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 296 through 300 removed outlier: 4.094A pdb=" N GLY B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 4.010A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.630A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 4.143A pdb=" N ALA B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.523A pdb=" N THR C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.604A pdb=" N GLN C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 171 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 216 through 231 removed outlier: 4.076A pdb=" N ILE C 220 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.727A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 295 removed outlier: 4.006A pdb=" N GLU C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLN C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 4.101A pdb=" N GLU C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 61 through 75 removed outlier: 3.903A pdb=" N ILE D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 120 through 143 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.584A pdb=" N ARG D 150 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.884A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.926A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.634A pdb=" N LEU D 272 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 296 through 300 removed outlier: 4.150A pdb=" N GLY D 299 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.341A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 313 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.611A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 76 through 86 Processing helix chain 'E' and resid 120 through 143 removed outlier: 3.825A pdb=" N GLN E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.725A pdb=" N ARG E 150 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 171 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 217 through 231 removed outlier: 4.316A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.909A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 removed outlier: 3.572A pdb=" N LEU E 272 " --> pdb=" O ASN E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 296 through 299 removed outlier: 3.786A pdb=" N GLY E 299 " --> pdb=" O GLY E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 306 through 313 removed outlier: 4.159A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 311 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 7.222A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.626A pdb=" N ILE A 33 " --> pdb=" O ASN A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.648A pdb=" N PHE A 111 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 102 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 109 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 7.071A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.972A pdb=" N ILE B 33 " --> pdb=" O ASN B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 104 removed outlier: 4.200A pdb=" N ASP B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 removed outlier: 7.165A pdb=" N ARG C 27 " --> pdb=" O HIS C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.599A pdb=" N ASN C 93 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 104 removed outlier: 3.532A pdb=" N GLN C 102 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 109 " --> pdb=" O GLN C 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 34 removed outlier: 6.554A pdb=" N ILE D 33 " --> pdb=" O ASN D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 104 removed outlier: 3.747A pdb=" N HIS D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 111 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 34 removed outlier: 6.438A pdb=" N ILE E 33 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 104 removed outlier: 3.525A pdb=" N PHE E 111 " --> pdb=" O HIS E 100 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 102 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET E 109 " --> pdb=" O GLN E 102 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5025 1.34 - 1.46: 3297 1.46 - 1.58: 7188 1.58 - 1.70: 65 1.70 - 1.82: 145 Bond restraints: 15720 Sorted by residual: bond pdb=" C ILE C 270 " pdb=" N MET C 271 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.39e-02 5.18e+03 4.55e+00 bond pdb=" CA MET C 271 " pdb=" C MET C 271 " ideal model delta sigma weight residual 1.524 1.493 0.030 1.59e-02 3.96e+03 3.61e+00 bond pdb=" CA SER A 231 " pdb=" C SER A 231 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.72e-02 3.38e+03 2.51e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.464 1.444 0.019 1.25e-02 6.40e+03 2.39e+00 bond pdb=" CA MET B 271 " pdb=" C MET B 271 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.12e+00 ... (remaining 15715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 20678 1.84 - 3.69: 543 3.69 - 5.53: 76 5.53 - 7.37: 14 7.37 - 9.22: 4 Bond angle restraints: 21315 Sorted by residual: angle pdb=" C GLU C 55 " pdb=" N ASP C 56 " pdb=" CA ASP C 56 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N VAL D 267 " pdb=" CA VAL D 267 " pdb=" C VAL D 267 " ideal model delta sigma weight residual 112.98 108.60 4.38 1.25e+00 6.40e-01 1.23e+01 angle pdb=" N ILE E 378 " pdb=" CA ILE E 378 " pdb=" C ILE E 378 " ideal model delta sigma weight residual 113.42 109.41 4.01 1.17e+00 7.31e-01 1.18e+01 angle pdb=" N VAL C 267 " pdb=" CA VAL C 267 " pdb=" C VAL C 267 " ideal model delta sigma weight residual 113.07 108.63 4.44 1.36e+00 5.41e-01 1.06e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 112.50 116.23 -3.73 1.16e+00 7.43e-01 1.03e+01 ... (remaining 21310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8507 17.60 - 35.19: 855 35.19 - 52.79: 156 52.79 - 70.39: 29 70.39 - 87.98: 53 Dihedral angle restraints: 9600 sinusoidal: 4165 harmonic: 5435 Sorted by residual: dihedral pdb=" CA ILE A 303 " pdb=" C ILE A 303 " pdb=" N LEU A 304 " pdb=" CA LEU A 304 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ILE B 303 " pdb=" C ILE B 303 " pdb=" N LEU B 304 " pdb=" CA LEU B 304 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE C 303 " pdb=" C ILE C 303 " pdb=" N LEU C 304 " pdb=" CA LEU C 304 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1811 0.049 - 0.098: 539 0.098 - 0.147: 92 0.147 - 0.196: 7 0.196 - 0.245: 1 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CB THR C 35 " pdb=" CA THR C 35 " pdb=" OG1 THR C 35 " pdb=" CG2 THR C 35 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA MET B 142 " pdb=" N MET B 142 " pdb=" C MET B 142 " pdb=" CB MET B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA MET C 271 " pdb=" N MET C 271 " pdb=" C MET C 271 " pdb=" CB MET C 271 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.84e-01 ... (remaining 2447 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 306 " 0.055 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 307 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 216 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 217 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 306 " -0.034 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 307 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.028 5.00e-02 4.00e+02 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 514 2.70 - 3.25: 16106 3.25 - 3.80: 24655 3.80 - 4.35: 31316 4.35 - 4.90: 52085 Nonbonded interactions: 124676 Sorted by model distance: nonbonded pdb=" OH TYR B 69 " pdb=" NH2 ARG B 73 " model vdw 2.154 3.120 nonbonded pdb=" OH TYR D 337 " pdb=" OP2 C I1004 " model vdw 2.160 3.040 nonbonded pdb=" O ASP B 31 " pdb=" NZ LYS B 91 " model vdw 2.162 3.120 nonbonded pdb=" OG SER E 32 " pdb=" O LYS E 91 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR E 135 " pdb=" NH1 ARG E 150 " model vdw 2.184 3.120 ... (remaining 124671 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 8.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.170 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 0.062 15720 Z= 0.400 Angle : 0.747 9.217 21315 Z= 0.420 Chirality : 0.046 0.245 2450 Planarity : 0.004 0.081 2620 Dihedral : 15.507 87.981 6130 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.19), residues: 1880 helix: 0.18 (0.15), residues: 1138 sheet: 1.49 (0.56), residues: 76 loop : -1.09 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 260 HIS 0.010 0.002 HIS E 216 PHE 0.014 0.002 PHE A 226 TYR 0.031 0.002 TYR D 301 ARG 0.008 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.611 Fit side-chains REVERT: A 50 MET cc_start: 0.8339 (mpp) cc_final: 0.8074 (mpp) REVERT: B 12 LEU cc_start: 0.8915 (tp) cc_final: 0.8483 (tp) REVERT: B 50 MET cc_start: 0.6837 (mpp) cc_final: 0.6388 (mpp) REVERT: C 67 MET cc_start: 0.8532 (mmm) cc_final: 0.7725 (mmt) REVERT: D 138 MET cc_start: 0.7424 (mtp) cc_final: 0.6628 (tmm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2796 time to fit residues: 79.3516 Evaluate side-chains 146 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 168 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN B 126 ASN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 151 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15720 Z= 0.206 Angle : 0.555 6.911 21315 Z= 0.294 Chirality : 0.041 0.195 2450 Planarity : 0.004 0.042 2620 Dihedral : 11.207 73.682 2590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.76 % Allowed : 8.63 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.25 (0.19), residues: 1880 helix: 0.75 (0.15), residues: 1156 sheet: 2.03 (0.62), residues: 68 loop : -1.01 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 260 HIS 0.007 0.001 HIS D 216 PHE 0.015 0.001 PHE E 219 TYR 0.016 0.001 TYR A 210 ARG 0.005 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.469 Fit side-chains REVERT: A 50 MET cc_start: 0.8315 (mpp) cc_final: 0.8102 (mpp) REVERT: B 50 MET cc_start: 0.6993 (mpp) cc_final: 0.6552 (mpp) REVERT: C 80 ILE cc_start: 0.6872 (mm) cc_final: 0.6591 (tp) REVERT: C 257 MET cc_start: 0.8362 (mmm) cc_final: 0.8047 (mmt) REVERT: D 138 MET cc_start: 0.7732 (mtp) cc_final: 0.6532 (tmm) outliers start: 12 outliers final: 9 residues processed: 178 average time/residue: 0.2738 time to fit residues: 73.9597 Evaluate side-chains 159 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 126 ASN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15720 Z= 0.288 Angle : 0.574 8.117 21315 Z= 0.300 Chirality : 0.042 0.177 2450 Planarity : 0.004 0.036 2620 Dihedral : 11.124 73.677 2590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.78 % Allowed : 11.56 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.31 (0.19), residues: 1880 helix: 0.79 (0.15), residues: 1160 sheet: 1.97 (0.63), residues: 68 loop : -0.98 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 260 HIS 0.014 0.002 HIS C 151 PHE 0.013 0.001 PHE A 226 TYR 0.016 0.002 TYR D 23 ARG 0.005 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.765 Fit side-chains REVERT: B 50 MET cc_start: 0.6783 (mpp) cc_final: 0.6520 (mtt) REVERT: B 256 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8133 (m) REVERT: C 80 ILE cc_start: 0.6962 (mm) cc_final: 0.6593 (tp) REVERT: C 257 MET cc_start: 0.8373 (mmm) cc_final: 0.7722 (mmt) REVERT: D 138 MET cc_start: 0.7749 (mtp) cc_final: 0.6602 (tmm) outliers start: 28 outliers final: 18 residues processed: 184 average time/residue: 0.2786 time to fit residues: 80.6487 Evaluate side-chains 165 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.7980 chunk 126 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 0.0980 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 126 ASN C 45 ASN C 89 HIS C 151 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15720 Z= 0.165 Angle : 0.505 8.659 21315 Z= 0.265 Chirality : 0.039 0.171 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.116 73.662 2590 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 12.83 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.69 (0.19), residues: 1880 helix: 1.09 (0.15), residues: 1163 sheet: 1.90 (0.62), residues: 68 loop : -0.78 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 260 HIS 0.011 0.001 HIS C 89 PHE 0.010 0.001 PHE D 226 TYR 0.011 0.001 TYR C 337 ARG 0.004 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 1.640 Fit side-chains REVERT: B 50 MET cc_start: 0.6718 (mpp) cc_final: 0.6395 (mtt) REVERT: B 175 ASP cc_start: 0.7116 (m-30) cc_final: 0.6689 (t0) REVERT: B 248 MET cc_start: 0.6927 (mmm) cc_final: 0.6604 (mtm) REVERT: B 256 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (m) REVERT: C 67 MET cc_start: 0.8562 (mmm) cc_final: 0.7717 (mmt) REVERT: C 80 ILE cc_start: 0.6915 (mm) cc_final: 0.6571 (tp) REVERT: C 201 LEU cc_start: 0.6756 (mp) cc_final: 0.6547 (tp) REVERT: D 27 ARG cc_start: 0.3117 (OUTLIER) cc_final: 0.1906 (mmp-170) REVERT: D 138 MET cc_start: 0.7765 (mtp) cc_final: 0.6652 (tmm) REVERT: E 12 LEU cc_start: 0.8627 (tt) cc_final: 0.8403 (tp) outliers start: 33 outliers final: 24 residues processed: 189 average time/residue: 0.2396 time to fit residues: 70.7134 Evaluate side-chains 185 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 133 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15720 Z= 0.184 Angle : 0.503 8.898 21315 Z= 0.263 Chirality : 0.040 0.151 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.079 73.630 2590 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.67 % Allowed : 13.52 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.19), residues: 1880 helix: 1.15 (0.15), residues: 1164 sheet: 1.89 (0.61), residues: 68 loop : -0.67 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 260 HIS 0.010 0.001 HIS C 89 PHE 0.011 0.001 PHE D 226 TYR 0.016 0.001 TYR C 337 ARG 0.004 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7174 (mm) REVERT: B 50 MET cc_start: 0.6728 (mpp) cc_final: 0.6416 (mtt) REVERT: B 88 TYR cc_start: 0.7947 (m-80) cc_final: 0.7505 (m-80) REVERT: B 175 ASP cc_start: 0.7149 (m-30) cc_final: 0.6676 (t70) REVERT: B 248 MET cc_start: 0.6928 (mmm) cc_final: 0.6641 (mtm) REVERT: B 256 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7971 (m) REVERT: C 80 ILE cc_start: 0.6912 (mm) cc_final: 0.6586 (tp) REVERT: D 27 ARG cc_start: 0.3197 (OUTLIER) cc_final: 0.1908 (mmp-170) REVERT: D 138 MET cc_start: 0.7749 (mtp) cc_final: 0.6961 (tmm) REVERT: E 12 LEU cc_start: 0.8615 (tt) cc_final: 0.8397 (tp) outliers start: 42 outliers final: 28 residues processed: 195 average time/residue: 0.2537 time to fit residues: 76.9546 Evaluate side-chains 185 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15720 Z= 0.182 Angle : 0.514 11.371 21315 Z= 0.264 Chirality : 0.039 0.147 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.060 73.622 2590 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.67 % Allowed : 13.84 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.20), residues: 1880 helix: 1.23 (0.15), residues: 1174 sheet: 1.85 (0.61), residues: 68 loop : -0.74 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 260 HIS 0.014 0.001 HIS C 89 PHE 0.010 0.001 PHE D 226 TYR 0.017 0.001 TYR B 353 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.743 Fit side-chains REVERT: A 83 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7150 (mm) REVERT: B 50 MET cc_start: 0.6714 (mpp) cc_final: 0.6429 (mtt) REVERT: B 88 TYR cc_start: 0.8012 (m-80) cc_final: 0.7468 (m-80) REVERT: B 175 ASP cc_start: 0.7122 (m-30) cc_final: 0.6688 (t0) REVERT: B 256 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7976 (m) REVERT: C 80 ILE cc_start: 0.6949 (mm) cc_final: 0.6587 (tp) REVERT: C 271 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7650 (mtm) REVERT: D 27 ARG cc_start: 0.3352 (OUTLIER) cc_final: 0.2003 (mmp-170) REVERT: D 138 MET cc_start: 0.7583 (mtp) cc_final: 0.6765 (tmm) REVERT: E 304 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7446 (mt) outliers start: 42 outliers final: 26 residues processed: 195 average time/residue: 0.2489 time to fit residues: 74.5352 Evaluate side-chains 184 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15720 Z= 0.196 Angle : 0.530 9.931 21315 Z= 0.270 Chirality : 0.040 0.150 2450 Planarity : 0.003 0.033 2620 Dihedral : 11.046 73.624 2590 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.54 % Allowed : 14.86 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.85 (0.19), residues: 1880 helix: 1.22 (0.15), residues: 1169 sheet: 1.69 (0.61), residues: 70 loop : -0.72 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 260 HIS 0.004 0.001 HIS C 225 PHE 0.010 0.001 PHE D 226 TYR 0.016 0.001 TYR C 337 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7177 (mm) REVERT: B 50 MET cc_start: 0.6683 (mpp) cc_final: 0.6431 (mtt) REVERT: B 175 ASP cc_start: 0.7048 (m-30) cc_final: 0.6582 (t70) REVERT: B 256 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7989 (m) REVERT: C 67 MET cc_start: 0.8559 (mmm) cc_final: 0.7538 (mmt) REVERT: C 80 ILE cc_start: 0.6958 (mm) cc_final: 0.6598 (tp) REVERT: C 271 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7655 (mtm) REVERT: D 138 MET cc_start: 0.7712 (mtp) cc_final: 0.6835 (tmm) REVERT: E 304 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7424 (mt) outliers start: 40 outliers final: 27 residues processed: 183 average time/residue: 0.2537 time to fit residues: 72.8733 Evaluate side-chains 187 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15720 Z= 0.202 Angle : 0.538 11.768 21315 Z= 0.273 Chirality : 0.040 0.148 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.035 73.624 2590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.16 % Allowed : 15.75 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.19), residues: 1880 helix: 1.21 (0.15), residues: 1170 sheet: 1.69 (0.62), residues: 70 loop : -0.68 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.008 0.001 HIS C 89 PHE 0.010 0.001 PHE D 226 TYR 0.016 0.001 TYR C 337 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.710 Fit side-chains REVERT: A 83 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7194 (mm) REVERT: B 50 MET cc_start: 0.6685 (mpp) cc_final: 0.6436 (mtt) REVERT: B 175 ASP cc_start: 0.6878 (m-30) cc_final: 0.6453 (t70) REVERT: B 256 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 26 GLN cc_start: 0.7156 (mt0) cc_final: 0.6945 (mt0) REVERT: C 67 MET cc_start: 0.8557 (mmm) cc_final: 0.7422 (mmt) REVERT: C 80 ILE cc_start: 0.6961 (mm) cc_final: 0.6601 (tp) REVERT: C 271 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7655 (mtm) REVERT: D 138 MET cc_start: 0.7707 (mtp) cc_final: 0.6833 (tmm) REVERT: E 304 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7473 (mt) outliers start: 34 outliers final: 26 residues processed: 180 average time/residue: 0.2407 time to fit residues: 69.1436 Evaluate side-chains 181 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15720 Z= 0.217 Angle : 0.544 11.518 21315 Z= 0.277 Chirality : 0.040 0.151 2450 Planarity : 0.003 0.033 2620 Dihedral : 11.020 73.629 2590 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.16 % Allowed : 16.32 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.82 (0.19), residues: 1880 helix: 1.16 (0.15), residues: 1170 sheet: 1.65 (0.61), residues: 70 loop : -0.68 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.005 0.001 HIS C 89 PHE 0.010 0.001 PHE D 226 TYR 0.017 0.001 TYR C 337 ARG 0.005 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.690 Fit side-chains REVERT: A 83 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7226 (mm) REVERT: A 142 MET cc_start: 0.6462 (pmm) cc_final: 0.6227 (pmm) REVERT: B 50 MET cc_start: 0.6701 (mpp) cc_final: 0.6480 (mtt) REVERT: B 256 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 67 MET cc_start: 0.8534 (mmm) cc_final: 0.7353 (mmt) REVERT: C 80 ILE cc_start: 0.6888 (mm) cc_final: 0.6459 (tp) REVERT: C 271 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: D 138 MET cc_start: 0.7707 (mtp) cc_final: 0.6826 (tmm) REVERT: E 304 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7439 (mt) outliers start: 34 outliers final: 27 residues processed: 180 average time/residue: 0.2433 time to fit residues: 69.2122 Evaluate side-chains 182 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 184 optimal weight: 0.0000 chunk 169 optimal weight: 0.0170 chunk 146 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15720 Z= 0.152 Angle : 0.541 12.377 21315 Z= 0.270 Chirality : 0.039 0.160 2450 Planarity : 0.003 0.031 2620 Dihedral : 11.056 73.611 2590 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.10 % Allowed : 16.51 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.99 (0.20), residues: 1880 helix: 1.30 (0.15), residues: 1174 sheet: 1.65 (0.62), residues: 70 loop : -0.59 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 260 HIS 0.011 0.001 HIS C 89 PHE 0.015 0.001 PHE B 61 TYR 0.016 0.001 TYR C 337 ARG 0.005 0.000 ARG B 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.796 Fit side-chains REVERT: A 83 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7100 (mm) REVERT: A 142 MET cc_start: 0.6338 (pmm) cc_final: 0.6093 (pmm) REVERT: B 50 MET cc_start: 0.6681 (mpp) cc_final: 0.6463 (mtt) REVERT: B 175 ASP cc_start: 0.7008 (m-30) cc_final: 0.6570 (t0) REVERT: B 256 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7830 (m) REVERT: C 80 ILE cc_start: 0.7083 (mm) cc_final: 0.6740 (tp) REVERT: C 271 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7603 (mtm) REVERT: D 138 MET cc_start: 0.7679 (mtp) cc_final: 0.6853 (tmm) outliers start: 33 outliers final: 27 residues processed: 186 average time/residue: 0.2352 time to fit residues: 69.6992 Evaluate side-chains 180 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.0570 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.199064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.169962 restraints weight = 21854.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.169605 restraints weight = 26721.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172137 restraints weight = 20278.951| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15720 Z= 0.170 Angle : 0.548 12.035 21315 Z= 0.279 Chirality : 0.039 0.203 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.053 73.622 2590 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 16.51 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.04 (0.20), residues: 1880 helix: 1.33 (0.15), residues: 1173 sheet: 1.71 (0.62), residues: 70 loop : -0.55 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 260 HIS 0.003 0.001 HIS A 225 PHE 0.011 0.001 PHE D 226 TYR 0.017 0.001 TYR C 337 ARG 0.005 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.96 seconds wall clock time: 53 minutes 26.28 seconds (3206.28 seconds total)