Starting phenix.real_space_refine on Wed Nov 19 00:17:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bo8_7120/11_2025/6bo8_7120.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bo8_7120/11_2025/6bo8_7120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bo8_7120/11_2025/6bo8_7120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bo8_7120/11_2025/6bo8_7120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bo8_7120/11_2025/6bo8_7120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bo8_7120/11_2025/6bo8_7120.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 4.51, per 1000 atoms: 0.24 Number of scatterers: 19048 At special positions: 0 Unit cell: (136.22, 136.22, 125.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3368 8.00 N 3220 7.00 C 12304 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: 1.59 Conformation dependent library (CDL) restraints added in 797.8 milliseconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.686A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.685A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.803A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.013A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.647A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.636A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.531A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 346 Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.190A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.010A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.570A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.527A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.688A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 587 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.637A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.547A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.775A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 492 Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 587 Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.92 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: 5464 1.33 - 1.45: 3323 1.45 - 1.57: 10433 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" CA VAL C 452 " pdb=" CB VAL C 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.97e+00 bond pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.93e+00 bond pdb=" CA VAL D 452 " pdb=" CB VAL D 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.69e+00 bond pdb=" CA HIS C 265 " pdb=" CB HIS C 265 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.63e+00 bond pdb=" CA VAL B 452 " pdb=" CB VAL B 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.63e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 25946 3.67 - 7.33: 434 7.33 - 11.00: 56 11.00 - 14.66: 0 14.66 - 18.33: 4 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N LEU D 352 " pdb=" CA LEU D 352 " pdb=" C LEU D 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU A 352 " pdb=" CA LEU A 352 " pdb=" C LEU A 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU C 352 " pdb=" CA LEU C 352 " pdb=" C LEU C 352 " ideal model delta sigma weight residual 110.91 118.00 -7.09 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.99 -7.08 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.52 -8.73 1.53e+00 4.27e-01 3.26e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 10858 15.42 - 30.85: 657 30.85 - 46.27: 157 46.27 - 61.69: 4 61.69 - 77.11: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASP B 223 " pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta harmonic sigma weight residual -180.00 -149.04 -30.96 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASP D 223 " pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2014 0.051 - 0.103: 827 0.103 - 0.154: 141 0.154 - 0.205: 19 0.205 - 0.256: 11 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ASP D 223 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP D 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG D 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ASP C 223 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C ASP A 223 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP A 223 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 224 " -0.015 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5470 2.81 - 3.33: 19064 3.33 - 3.85: 31397 3.85 - 4.38: 37260 4.38 - 4.90: 60177 Nonbonded interactions: 153368 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.310 3.040 ... (remaining 153363 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.530 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.050 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.008 0.065 19484 Z= 0.368 Angle : 1.192 18.330 26440 Z= 0.668 Chirality : 0.055 0.256 3012 Planarity : 0.007 0.049 3336 Dihedral : 10.831 77.114 7184 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.97 % Allowed : 2.13 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.14), residues: 2356 helix: -2.68 (0.10), residues: 1344 sheet: -5.00 (0.44), residues: 56 loop : -3.13 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 305 TYR 0.026 0.003 TYR C 547 PHE 0.029 0.003 PHE D 169 TRP 0.026 0.004 TRP D 629 HIS 0.017 0.003 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00754 (19484) covalent geometry : angle 1.19203 (26440) hydrogen bonds : bond 0.28238 ( 884) hydrogen bonds : angle 8.55933 ( 2532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 759 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.7568 (m) cc_final: 0.6918 (p) REVERT: A 183 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7377 (mm) REVERT: A 246 LEU cc_start: 0.6794 (tp) cc_final: 0.6588 (tp) REVERT: A 252 ASN cc_start: 0.6715 (t0) cc_final: 0.6322 (t0) REVERT: A 262 LYS cc_start: 0.8358 (tptp) cc_final: 0.7767 (mttt) REVERT: A 382 ASP cc_start: 0.7143 (m-30) cc_final: 0.6723 (m-30) REVERT: A 383 ASP cc_start: 0.8301 (m-30) cc_final: 0.7916 (t0) REVERT: A 435 MET cc_start: 0.6735 (mmt) cc_final: 0.6409 (mmt) REVERT: A 464 ASN cc_start: 0.6570 (t160) cc_final: 0.6253 (m-40) REVERT: A 487 PHE cc_start: 0.7586 (m-80) cc_final: 0.7338 (m-10) REVERT: A 527 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8103 (Cg_endo) REVERT: A 550 ASP cc_start: 0.8049 (t0) cc_final: 0.7022 (p0) REVERT: A 580 ASP cc_start: 0.6486 (t0) cc_final: 0.6159 (m-30) REVERT: A 590 ASP cc_start: 0.7360 (m-30) cc_final: 0.6874 (t0) REVERT: A 628 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7817 (mtp-110) REVERT: A 630 PHE cc_start: 0.6910 (m-80) cc_final: 0.6499 (m-80) REVERT: B 40 GLN cc_start: 0.7590 (tt0) cc_final: 0.7276 (tt0) REVERT: B 78 MET cc_start: 0.7142 (pmt) cc_final: 0.6848 (pmm) REVERT: B 80 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8255 (mt-10) REVERT: B 97 VAL cc_start: 0.8799 (t) cc_final: 0.8574 (t) REVERT: B 106 VAL cc_start: 0.8541 (t) cc_final: 0.8317 (p) REVERT: B 176 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 183 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7285 (mm) REVERT: B 235 VAL cc_start: 0.7909 (t) cc_final: 0.7603 (m) REVERT: B 252 ASN cc_start: 0.6490 (t0) cc_final: 0.6117 (t0) REVERT: B 262 LYS cc_start: 0.8342 (tptp) cc_final: 0.7816 (mttt) REVERT: B 328 TYR cc_start: 0.6103 (m-10) cc_final: 0.5805 (m-10) REVERT: B 332 LEU cc_start: 0.6211 (tp) cc_final: 0.5993 (mt) REVERT: B 435 MET cc_start: 0.6695 (mmt) cc_final: 0.6441 (mmt) REVERT: B 450 GLU cc_start: 0.6692 (pt0) cc_final: 0.6366 (pt0) REVERT: B 527 PRO cc_start: 0.8627 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: B 550 ASP cc_start: 0.7753 (t0) cc_final: 0.6641 (p0) REVERT: B 588 GLU cc_start: 0.7042 (pt0) cc_final: 0.6836 (pt0) REVERT: B 590 ASP cc_start: 0.6970 (m-30) cc_final: 0.6519 (t0) REVERT: B 628 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7660 (mtp-110) REVERT: B 630 PHE cc_start: 0.6582 (m-80) cc_final: 0.6141 (m-80) REVERT: C 40 GLN cc_start: 0.7669 (tt0) cc_final: 0.7412 (tt0) REVERT: C 78 MET cc_start: 0.7233 (pmt) cc_final: 0.6951 (pmm) REVERT: C 80 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8118 (mt-10) REVERT: C 97 VAL cc_start: 0.8824 (t) cc_final: 0.8596 (t) REVERT: C 160 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 176 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8041 (mp0) REVERT: C 183 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7759 (mp) REVERT: C 202 ILE cc_start: 0.8042 (mm) cc_final: 0.7798 (mm) REVERT: C 214 GLN cc_start: 0.7430 (tt0) cc_final: 0.7115 (tm-30) REVERT: C 217 ASN cc_start: 0.7381 (m-40) cc_final: 0.6998 (m-40) REVERT: C 235 VAL cc_start: 0.8006 (t) cc_final: 0.7606 (m) REVERT: C 252 ASN cc_start: 0.6847 (t0) cc_final: 0.6589 (t0) REVERT: C 262 LYS cc_start: 0.8013 (tptp) cc_final: 0.7402 (mttt) REVERT: C 331 MET cc_start: 0.6016 (tmm) cc_final: 0.5798 (tmm) REVERT: C 435 MET cc_start: 0.6241 (mmt) cc_final: 0.5944 (mmt) REVERT: C 467 TYR cc_start: 0.7290 (t80) cc_final: 0.7081 (t80) REVERT: C 474 MET cc_start: 0.6346 (mmm) cc_final: 0.5995 (ptt) REVERT: C 482 ILE cc_start: 0.6419 (mm) cc_final: 0.6081 (mt) REVERT: C 550 ASP cc_start: 0.7377 (t0) cc_final: 0.6600 (p0) REVERT: C 565 ILE cc_start: 0.7459 (tp) cc_final: 0.7019 (mm) REVERT: C 580 ASP cc_start: 0.6441 (t0) cc_final: 0.5967 (m-30) REVERT: C 583 TRP cc_start: 0.6997 (t60) cc_final: 0.6172 (t60) REVERT: C 591 GLU cc_start: 0.6536 (tt0) cc_final: 0.6220 (tp30) REVERT: C 630 PHE cc_start: 0.6519 (m-80) cc_final: 0.6299 (m-80) REVERT: D 44 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7127 (mp) REVERT: D 78 MET cc_start: 0.7339 (pmt) cc_final: 0.6983 (pmm) REVERT: D 157 CYS cc_start: 0.7881 (m) cc_final: 0.7281 (p) REVERT: D 183 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7650 (mm) REVERT: D 214 GLN cc_start: 0.7416 (tt0) cc_final: 0.7033 (tm-30) REVERT: D 252 ASN cc_start: 0.6554 (t0) cc_final: 0.6155 (t0) REVERT: D 262 LYS cc_start: 0.8305 (tptp) cc_final: 0.7648 (mttt) REVERT: D 265 HIS cc_start: 0.6581 (t70) cc_final: 0.6369 (t70) REVERT: D 328 TYR cc_start: 0.6045 (m-10) cc_final: 0.5785 (m-10) REVERT: D 384 ILE cc_start: 0.7764 (mt) cc_final: 0.7527 (mp) REVERT: D 464 ASN cc_start: 0.6722 (t160) cc_final: 0.6374 (t0) REVERT: D 487 PHE cc_start: 0.7493 (m-80) cc_final: 0.7250 (m-10) REVERT: D 550 ASP cc_start: 0.7811 (t0) cc_final: 0.7168 (p0) REVERT: D 580 ASP cc_start: 0.6471 (t0) cc_final: 0.6163 (m-30) REVERT: D 590 ASP cc_start: 0.7208 (m-30) cc_final: 0.6883 (t0) REVERT: D 634 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8279 (mm-30) outliers start: 20 outliers final: 0 residues processed: 769 average time/residue: 0.1486 time to fit residues: 171.2556 Evaluate side-chains 472 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 466 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 183 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS B 165 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 546 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 265 HIS C 464 ASN C 522 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 522 HIS D 548 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131276 restraints weight = 28633.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134127 restraints weight = 16136.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135960 restraints weight = 11349.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137045 restraints weight = 9165.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137586 restraints weight = 8090.747| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19484 Z= 0.148 Angle : 0.747 11.933 26440 Z= 0.374 Chirality : 0.043 0.208 3012 Planarity : 0.005 0.043 3336 Dihedral : 6.088 39.285 2608 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.42 % Favored : 90.41 % Rotamer: Outliers : 2.52 % Allowed : 12.84 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.16), residues: 2356 helix: -0.51 (0.13), residues: 1356 sheet: -4.34 (0.49), residues: 56 loop : -2.66 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 323 TYR 0.015 0.001 TYR C 526 PHE 0.018 0.002 PHE B 553 TRP 0.016 0.002 TRP B 629 HIS 0.007 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00324 (19484) covalent geometry : angle 0.74716 (26440) hydrogen bonds : bond 0.04543 ( 884) hydrogen bonds : angle 4.40004 ( 2532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 531 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.7761 (m-40) cc_final: 0.7404 (m-40) REVERT: A 435 MET cc_start: 0.7545 (mmt) cc_final: 0.7123 (mmt) REVERT: A 482 ILE cc_start: 0.8763 (mm) cc_final: 0.8484 (mm) REVERT: A 550 ASP cc_start: 0.7848 (t0) cc_final: 0.7421 (p0) REVERT: A 580 ASP cc_start: 0.7901 (t0) cc_final: 0.7596 (m-30) REVERT: B 96 MET cc_start: 0.7867 (mmm) cc_final: 0.7640 (mmm) REVERT: B 378 MET cc_start: 0.6624 (pmm) cc_final: 0.6393 (pmm) REVERT: B 435 MET cc_start: 0.7184 (mmt) cc_final: 0.6722 (mmt) REVERT: B 502 LEU cc_start: 0.8933 (mm) cc_final: 0.8497 (mt) REVERT: B 524 TYR cc_start: 0.7697 (p90) cc_final: 0.7412 (p90) REVERT: B 528 MET cc_start: 0.8258 (tmm) cc_final: 0.7790 (tmm) REVERT: C 331 MET cc_start: 0.6915 (tmm) cc_final: 0.6666 (tmm) REVERT: C 435 MET cc_start: 0.7191 (mmt) cc_final: 0.6926 (mmt) REVERT: C 467 TYR cc_start: 0.8498 (t80) cc_final: 0.8287 (t80) REVERT: C 528 MET cc_start: 0.8132 (tmm) cc_final: 0.7906 (tpp) REVERT: C 540 ILE cc_start: 0.8337 (mm) cc_final: 0.8087 (mt) REVERT: C 565 ILE cc_start: 0.9107 (tp) cc_final: 0.8586 (mm) REVERT: C 580 ASP cc_start: 0.8036 (t0) cc_final: 0.7551 (m-30) REVERT: D 158 ASN cc_start: 0.7778 (m-40) cc_final: 0.7437 (m-40) outliers start: 52 outliers final: 24 residues processed: 567 average time/residue: 0.1307 time to fit residues: 116.7270 Evaluate side-chains 412 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 388 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 265 HIS B 267 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127738 restraints weight = 28708.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130591 restraints weight = 15972.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132411 restraints weight = 11209.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133537 restraints weight = 9023.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134081 restraints weight = 7933.627| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19484 Z= 0.143 Angle : 0.732 11.845 26440 Z= 0.359 Chirality : 0.043 0.232 3012 Planarity : 0.004 0.043 3336 Dihedral : 5.317 30.560 2596 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.54 % Allowed : 16.23 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2356 helix: 0.27 (0.14), residues: 1360 sheet: -3.80 (0.54), residues: 56 loop : -2.59 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 263 TYR 0.026 0.001 TYR C 324 PHE 0.023 0.002 PHE B 244 TRP 0.011 0.001 TRP C 321 HIS 0.019 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00320 (19484) covalent geometry : angle 0.73198 (26440) hydrogen bonds : bond 0.03886 ( 884) hydrogen bonds : angle 4.09688 ( 2532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 454 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 158 ASN cc_start: 0.7705 (m-40) cc_final: 0.7504 (m-40) REVERT: A 435 MET cc_start: 0.7572 (mmt) cc_final: 0.7209 (mmt) REVERT: A 483 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5025 (tp40) REVERT: A 550 ASP cc_start: 0.7854 (t0) cc_final: 0.7368 (p0) REVERT: A 580 ASP cc_start: 0.7991 (t0) cc_final: 0.7551 (m-30) REVERT: B 96 MET cc_start: 0.7916 (mmm) cc_final: 0.7680 (mmm) REVERT: B 368 LEU cc_start: 0.7725 (pp) cc_final: 0.7497 (pp) REVERT: B 435 MET cc_start: 0.7391 (mmt) cc_final: 0.6918 (mmt) REVERT: B 502 LEU cc_start: 0.8888 (mm) cc_final: 0.8538 (mt) REVERT: B 540 ILE cc_start: 0.8826 (mm) cc_final: 0.8570 (mm) REVERT: B 550 ASP cc_start: 0.7617 (t0) cc_final: 0.6939 (p0) REVERT: B 630 PHE cc_start: 0.8511 (m-80) cc_final: 0.8197 (m-80) REVERT: C 435 MET cc_start: 0.7208 (mmt) cc_final: 0.6936 (mmt) REVERT: C 464 ASN cc_start: 0.8280 (t160) cc_final: 0.8078 (t0) REVERT: C 467 TYR cc_start: 0.8627 (t80) cc_final: 0.8374 (t80) REVERT: C 565 ILE cc_start: 0.9162 (tp) cc_final: 0.8676 (mm) REVERT: C 570 MET cc_start: 0.7856 (mtt) cc_final: 0.7638 (mtp) REVERT: C 580 ASP cc_start: 0.8040 (t0) cc_final: 0.7579 (m-30) REVERT: D 118 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: D 158 ASN cc_start: 0.7647 (m-40) cc_final: 0.7368 (m-40) outliers start: 73 outliers final: 39 residues processed: 500 average time/residue: 0.1178 time to fit residues: 96.0440 Evaluate side-chains 425 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 384 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 50 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 91 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 265 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 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 = 0.3790 r_free = 0.3790 target = 0.157866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129183 restraints weight = 28573.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132020 restraints weight = 16171.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133802 restraints weight = 11348.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134752 restraints weight = 9161.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135474 restraints weight = 8119.052| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19484 Z= 0.123 Angle : 0.692 13.417 26440 Z= 0.337 Chirality : 0.041 0.214 3012 Planarity : 0.004 0.043 3336 Dihedral : 5.056 28.889 2596 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 3.88 % Allowed : 17.01 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2356 helix: 0.59 (0.14), residues: 1368 sheet: -3.58 (0.56), residues: 56 loop : -2.52 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 305 TYR 0.026 0.001 TYR D 324 PHE 0.017 0.001 PHE B 531 TRP 0.009 0.001 TRP C 321 HIS 0.009 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00266 (19484) covalent geometry : angle 0.69167 (26440) hydrogen bonds : bond 0.03406 ( 884) hydrogen bonds : angle 3.88218 ( 2532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 434 time to evaluate : 0.589 Fit side-chains REVERT: A 80 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 96 MET cc_start: 0.7389 (mmm) cc_final: 0.7057 (mmm) REVERT: A 118 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: A 158 ASN cc_start: 0.7593 (m-40) cc_final: 0.7319 (m-40) REVERT: A 435 MET cc_start: 0.7546 (mmt) cc_final: 0.7171 (mmt) REVERT: A 483 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5003 (tp40) REVERT: A 550 ASP cc_start: 0.7855 (t0) cc_final: 0.7374 (p0) REVERT: A 580 ASP cc_start: 0.7906 (t0) cc_final: 0.7479 (m-30) REVERT: B 78 MET cc_start: 0.6233 (pmm) cc_final: 0.5861 (pmm) REVERT: B 352 LEU cc_start: 0.7878 (mp) cc_final: 0.7625 (mp) REVERT: B 435 MET cc_start: 0.7424 (mmt) cc_final: 0.6991 (mmt) REVERT: B 540 ILE cc_start: 0.8800 (mm) cc_final: 0.8569 (mm) REVERT: B 550 ASP cc_start: 0.7681 (t0) cc_final: 0.7112 (p0) REVERT: B 554 MET cc_start: 0.8528 (tpt) cc_final: 0.8313 (tpp) REVERT: B 630 PHE cc_start: 0.8465 (m-80) cc_final: 0.8146 (m-80) REVERT: C 252 ASN cc_start: 0.8685 (t0) cc_final: 0.8160 (t0) REVERT: C 435 MET cc_start: 0.7302 (mmt) cc_final: 0.7022 (mmt) REVERT: C 565 ILE cc_start: 0.9111 (tp) cc_final: 0.8635 (mm) REVERT: C 580 ASP cc_start: 0.7926 (t0) cc_final: 0.7513 (m-30) REVERT: D 588 GLU cc_start: 0.8000 (pt0) cc_final: 0.7753 (pt0) outliers start: 80 outliers final: 46 residues processed: 484 average time/residue: 0.1216 time to fit residues: 94.9039 Evaluate side-chains 422 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 38 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN B 265 HIS B 522 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 206 GLN C 464 ASN C 546 ASN D 370 GLN D 464 ASN D 546 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127074 restraints weight = 28560.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129909 restraints weight = 15974.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131710 restraints weight = 11215.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132795 restraints weight = 9041.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133477 restraints weight = 7958.681| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19484 Z= 0.129 Angle : 0.694 12.796 26440 Z= 0.336 Chirality : 0.042 0.249 3012 Planarity : 0.004 0.042 3336 Dihedral : 4.901 28.718 2596 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 4.17 % Allowed : 17.73 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2356 helix: 0.81 (0.14), residues: 1372 sheet: -3.36 (0.57), residues: 56 loop : -2.45 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 305 TYR 0.023 0.001 TYR D 324 PHE 0.014 0.001 PHE A 478 TRP 0.009 0.001 TRP C 321 HIS 0.014 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00288 (19484) covalent geometry : angle 0.69442 (26440) hydrogen bonds : bond 0.03322 ( 884) hydrogen bonds : angle 3.80629 ( 2532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 406 time to evaluate : 0.742 Fit side-chains REVERT: A 80 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 96 MET cc_start: 0.7323 (mmm) cc_final: 0.7100 (mmm) REVERT: A 158 ASN cc_start: 0.7549 (m-40) cc_final: 0.7288 (m-40) REVERT: A 435 MET cc_start: 0.7625 (mmt) cc_final: 0.7248 (mmt) REVERT: A 483 GLN cc_start: 0.6235 (OUTLIER) cc_final: 0.4879 (tp40) REVERT: A 550 ASP cc_start: 0.7883 (t0) cc_final: 0.7390 (p0) REVERT: A 580 ASP cc_start: 0.7862 (t0) cc_final: 0.7449 (m-30) REVERT: B 78 MET cc_start: 0.6431 (pmm) cc_final: 0.6182 (pmm) REVERT: B 96 MET cc_start: 0.7474 (mmm) cc_final: 0.7154 (mmm) REVERT: B 531 PHE cc_start: 0.8765 (t80) cc_final: 0.8231 (t80) REVERT: B 550 ASP cc_start: 0.7669 (t0) cc_final: 0.7150 (p0) REVERT: B 630 PHE cc_start: 0.8554 (m-80) cc_final: 0.8285 (m-80) REVERT: C 100 GLU cc_start: 0.7317 (mp0) cc_final: 0.6962 (pm20) REVERT: C 252 ASN cc_start: 0.8809 (t0) cc_final: 0.8260 (t0) REVERT: C 435 MET cc_start: 0.7357 (mmt) cc_final: 0.7140 (mmt) REVERT: C 496 LEU cc_start: 0.9226 (tp) cc_final: 0.9022 (mt) REVERT: C 565 ILE cc_start: 0.9132 (tp) cc_final: 0.8643 (mm) REVERT: C 580 ASP cc_start: 0.7956 (t0) cc_final: 0.7465 (m-30) REVERT: D 96 MET cc_start: 0.7563 (mmp) cc_final: 0.6986 (mmm) REVERT: D 118 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7105 (tt0) outliers start: 86 outliers final: 47 residues processed: 456 average time/residue: 0.1201 time to fit residues: 88.2649 Evaluate side-chains 415 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 366 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 169 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 267 GLN A 546 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125494 restraints weight = 28434.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128390 restraints weight = 15834.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130199 restraints weight = 11052.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131314 restraints weight = 8893.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131724 restraints weight = 7811.650| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19484 Z= 0.135 Angle : 0.690 11.469 26440 Z= 0.335 Chirality : 0.042 0.205 3012 Planarity : 0.004 0.042 3336 Dihedral : 4.807 28.226 2596 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.68 % Allowed : 18.60 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2356 helix: 0.93 (0.14), residues: 1372 sheet: -3.28 (0.55), residues: 56 loop : -2.42 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 224 TYR 0.026 0.001 TYR B 524 PHE 0.016 0.001 PHE A 244 TRP 0.009 0.001 TRP C 321 HIS 0.006 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00307 (19484) covalent geometry : angle 0.69027 (26440) hydrogen bonds : bond 0.03316 ( 884) hydrogen bonds : angle 3.81179 ( 2532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 391 time to evaluate : 0.718 Fit side-chains REVERT: A 80 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 96 MET cc_start: 0.7382 (mmm) cc_final: 0.7117 (mmm) REVERT: A 118 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: A 158 ASN cc_start: 0.7560 (m-40) cc_final: 0.7326 (m-40) REVERT: A 345 MET cc_start: 0.8263 (mmm) cc_final: 0.8040 (mmm) REVERT: A 435 MET cc_start: 0.7622 (mmt) cc_final: 0.7281 (mmt) REVERT: A 456 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: A 483 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.4674 (tp40) REVERT: A 550 ASP cc_start: 0.7896 (t0) cc_final: 0.7460 (p0) REVERT: B 96 MET cc_start: 0.7546 (mmm) cc_final: 0.7224 (mmm) REVERT: B 118 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: B 550 ASP cc_start: 0.7732 (t0) cc_final: 0.7248 (p0) REVERT: B 630 PHE cc_start: 0.8616 (m-80) cc_final: 0.8334 (m-80) REVERT: C 252 ASN cc_start: 0.8893 (t0) cc_final: 0.8375 (t0) REVERT: C 435 MET cc_start: 0.7472 (mmt) cc_final: 0.7242 (mmt) REVERT: C 565 ILE cc_start: 0.9178 (tp) cc_final: 0.8714 (mm) REVERT: C 580 ASP cc_start: 0.7945 (t0) cc_final: 0.7506 (m-30) REVERT: D 96 MET cc_start: 0.7670 (mmp) cc_final: 0.7073 (mmm) REVERT: D 100 GLU cc_start: 0.7413 (mp0) cc_final: 0.7077 (pm20) REVERT: D 118 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: D 158 ASN cc_start: 0.7449 (m-40) cc_final: 0.7221 (m-40) outliers start: 76 outliers final: 47 residues processed: 443 average time/residue: 0.1253 time to fit residues: 89.2749 Evaluate side-chains 416 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 364 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 227 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 169 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 265 HIS A 546 ASN B 596 GLN C 118 GLN D 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129026 restraints weight = 28307.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131957 restraints weight = 15697.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133824 restraints weight = 10912.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134975 restraints weight = 8753.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135475 restraints weight = 7682.236| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19484 Z= 0.118 Angle : 0.688 12.957 26440 Z= 0.330 Chirality : 0.041 0.223 3012 Planarity : 0.004 0.039 3336 Dihedral : 4.686 28.215 2596 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.25 % Allowed : 19.38 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2356 helix: 1.04 (0.14), residues: 1372 sheet: -3.13 (0.55), residues: 56 loop : -2.36 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 224 TYR 0.024 0.001 TYR A 324 PHE 0.017 0.001 PHE B 244 TRP 0.008 0.001 TRP B 462 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00257 (19484) covalent geometry : angle 0.68757 (26440) hydrogen bonds : bond 0.03097 ( 884) hydrogen bonds : angle 3.76238 ( 2532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 398 time to evaluate : 0.748 Fit side-chains REVERT: A 78 MET cc_start: 0.6179 (pmm) cc_final: 0.5801 (pmm) REVERT: A 96 MET cc_start: 0.7389 (mmm) cc_final: 0.7176 (mmm) REVERT: A 158 ASN cc_start: 0.7497 (m-40) cc_final: 0.7283 (m-40) REVERT: A 345 MET cc_start: 0.8264 (mmm) cc_final: 0.8041 (mmm) REVERT: A 456 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: A 483 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.4697 (tp40) REVERT: A 550 ASP cc_start: 0.7750 (t0) cc_final: 0.7480 (p0) REVERT: B 96 MET cc_start: 0.7577 (mmm) cc_final: 0.7201 (mmm) REVERT: B 331 MET cc_start: 0.6668 (tmm) cc_final: 0.6326 (tmm) REVERT: B 550 ASP cc_start: 0.7711 (t0) cc_final: 0.7280 (p0) REVERT: B 630 PHE cc_start: 0.8527 (m-80) cc_final: 0.8290 (m-80) REVERT: C 96 MET cc_start: 0.7555 (mmm) cc_final: 0.7263 (mmm) REVERT: C 252 ASN cc_start: 0.8855 (t0) cc_final: 0.8322 (t0) REVERT: C 371 LYS cc_start: 0.7572 (mttt) cc_final: 0.6940 (mtmt) REVERT: C 565 ILE cc_start: 0.9087 (tp) cc_final: 0.8615 (mm) REVERT: D 118 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: D 174 ASN cc_start: 0.8183 (t0) cc_final: 0.7974 (t0) outliers start: 67 outliers final: 49 residues processed: 440 average time/residue: 0.1269 time to fit residues: 88.8166 Evaluate side-chains 424 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 372 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 132 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 118 GLN ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.115411 restraints weight = 28729.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118228 restraints weight = 16126.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120046 restraints weight = 11300.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121148 restraints weight = 9072.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121862 restraints weight = 7966.120| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19484 Z= 0.266 Angle : 0.813 13.985 26440 Z= 0.402 Chirality : 0.047 0.225 3012 Planarity : 0.005 0.056 3336 Dihedral : 5.027 27.091 2596 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 4.02 % Allowed : 19.19 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2356 helix: 0.79 (0.14), residues: 1372 sheet: -3.11 (0.53), residues: 56 loop : -2.40 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 224 TYR 0.025 0.002 TYR A 324 PHE 0.026 0.003 PHE D 478 TRP 0.012 0.002 TRP C 321 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00633 (19484) covalent geometry : angle 0.81332 (26440) hydrogen bonds : bond 0.04107 ( 884) hydrogen bonds : angle 4.19773 ( 2532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 376 time to evaluate : 0.768 Fit side-chains REVERT: A 158 ASN cc_start: 0.7842 (m-40) cc_final: 0.7590 (m110) REVERT: A 264 LYS cc_start: 0.8235 (pttt) cc_final: 0.7999 (pttm) REVERT: A 345 MET cc_start: 0.8238 (mmm) cc_final: 0.8019 (mmp) REVERT: A 467 TYR cc_start: 0.8812 (t80) cc_final: 0.8570 (t80) REVERT: A 483 GLN cc_start: 0.6136 (OUTLIER) cc_final: 0.4795 (tp40) REVERT: A 550 ASP cc_start: 0.7785 (t0) cc_final: 0.7509 (p0) REVERT: B 118 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: B 264 LYS cc_start: 0.8353 (pttt) cc_final: 0.8066 (pttm) REVERT: B 345 MET cc_start: 0.8069 (mmm) cc_final: 0.7829 (mmp) REVERT: B 389 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: B 467 TYR cc_start: 0.8816 (t80) cc_final: 0.8547 (t80) REVERT: B 550 ASP cc_start: 0.7735 (t0) cc_final: 0.7444 (p0) REVERT: B 580 ASP cc_start: 0.7971 (t0) cc_final: 0.7471 (m-30) REVERT: C 371 LYS cc_start: 0.7954 (mttt) cc_final: 0.7172 (mttt) REVERT: C 467 TYR cc_start: 0.8848 (t80) cc_final: 0.8598 (t80) REVERT: D 100 GLU cc_start: 0.7487 (mp0) cc_final: 0.7245 (pm20) REVERT: D 130 MET cc_start: 0.7763 (mmt) cc_final: 0.7526 (tpt) REVERT: D 158 ASN cc_start: 0.7814 (m-40) cc_final: 0.7503 (m-40) outliers start: 83 outliers final: 52 residues processed: 435 average time/residue: 0.1284 time to fit residues: 87.7744 Evaluate side-chains 399 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 344 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 208 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 546 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 546 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 = 0.3710 r_free = 0.3710 target = 0.151330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121719 restraints weight = 28254.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124721 restraints weight = 15570.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126604 restraints weight = 10718.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127761 restraints weight = 8577.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128440 restraints weight = 7502.296| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19484 Z= 0.133 Angle : 0.729 11.358 26440 Z= 0.352 Chirality : 0.043 0.226 3012 Planarity : 0.004 0.052 3336 Dihedral : 4.825 28.369 2596 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 2.81 % Allowed : 20.40 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2356 helix: 0.99 (0.14), residues: 1360 sheet: -3.02 (0.53), residues: 56 loop : -2.36 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 305 TYR 0.024 0.001 TYR A 324 PHE 0.020 0.001 PHE D 478 TRP 0.010 0.001 TRP C 321 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00300 (19484) covalent geometry : angle 0.72934 (26440) hydrogen bonds : bond 0.03392 ( 884) hydrogen bonds : angle 3.95729 ( 2532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 0.717 Fit side-chains REVERT: A 158 ASN cc_start: 0.7760 (m-40) cc_final: 0.7539 (m-40) REVERT: A 264 LYS cc_start: 0.8094 (pttt) cc_final: 0.7894 (pttm) REVERT: A 345 MET cc_start: 0.8308 (mmm) cc_final: 0.8071 (mmp) REVERT: A 483 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.4848 (tp40) REVERT: A 550 ASP cc_start: 0.7619 (t0) cc_final: 0.7373 (p0) REVERT: B 96 MET cc_start: 0.7572 (mmm) cc_final: 0.7214 (mmm) REVERT: B 118 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: B 130 MET cc_start: 0.7618 (mmt) cc_final: 0.7268 (tpt) REVERT: B 264 LYS cc_start: 0.8146 (pttt) cc_final: 0.7928 (pttm) REVERT: B 345 MET cc_start: 0.8064 (mmm) cc_final: 0.7808 (mmp) REVERT: B 389 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: B 550 ASP cc_start: 0.7633 (t0) cc_final: 0.7396 (p0) REVERT: C 100 GLU cc_start: 0.7417 (mp0) cc_final: 0.7084 (pm20) REVERT: C 371 LYS cc_start: 0.7783 (mttt) cc_final: 0.7020 (mtmt) REVERT: D 100 GLU cc_start: 0.7385 (mp0) cc_final: 0.7131 (pm20) REVERT: D 158 ASN cc_start: 0.7605 (m-40) cc_final: 0.7341 (m110) REVERT: D 174 ASN cc_start: 0.8529 (t0) cc_final: 0.8262 (t0) REVERT: D 615 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7982 (mtp-110) outliers start: 58 outliers final: 44 residues processed: 406 average time/residue: 0.1328 time to fit residues: 84.8799 Evaluate side-chains 394 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 346 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 4 optimal weight: 20.0000 chunk 193 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 91 optimal weight: 0.0030 chunk 165 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN D 464 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121777 restraints weight = 28435.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124742 restraints weight = 15764.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126621 restraints weight = 10906.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127626 restraints weight = 8724.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128453 restraints weight = 7694.892| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19484 Z= 0.141 Angle : 0.730 13.359 26440 Z= 0.353 Chirality : 0.043 0.222 3012 Planarity : 0.004 0.050 3336 Dihedral : 4.741 27.765 2596 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 2.66 % Allowed : 21.37 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2356 helix: 1.02 (0.14), residues: 1364 sheet: -2.95 (0.53), residues: 56 loop : -2.32 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 224 TYR 0.026 0.001 TYR A 324 PHE 0.015 0.001 PHE B 534 TRP 0.009 0.001 TRP C 321 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00327 (19484) covalent geometry : angle 0.73011 (26440) hydrogen bonds : bond 0.03406 ( 884) hydrogen bonds : angle 3.99210 ( 2532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 0.792 Fit side-chains REVERT: A 158 ASN cc_start: 0.7738 (m-40) cc_final: 0.7529 (m-40) REVERT: A 345 MET cc_start: 0.8304 (mmm) cc_final: 0.8066 (mmp) REVERT: A 483 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.4876 (tp40) REVERT: A 550 ASP cc_start: 0.7524 (t0) cc_final: 0.7275 (p0) REVERT: B 96 MET cc_start: 0.7548 (mmm) cc_final: 0.7085 (mmm) REVERT: B 100 GLU cc_start: 0.7450 (mp0) cc_final: 0.7085 (pm20) REVERT: B 118 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: B 345 MET cc_start: 0.8045 (mmm) cc_final: 0.7805 (mmp) REVERT: B 580 ASP cc_start: 0.7999 (t0) cc_final: 0.7075 (m-30) REVERT: C 100 GLU cc_start: 0.7393 (mp0) cc_final: 0.7078 (pm20) REVERT: C 371 LYS cc_start: 0.7816 (mttt) cc_final: 0.7005 (mtmt) REVERT: D 78 MET cc_start: 0.5782 (pmm) cc_final: 0.5131 (pmm) REVERT: D 100 GLU cc_start: 0.7349 (mp0) cc_final: 0.7121 (pm20) REVERT: D 158 ASN cc_start: 0.7576 (m-40) cc_final: 0.7311 (m110) REVERT: D 174 ASN cc_start: 0.8513 (t0) cc_final: 0.8283 (t0) outliers start: 55 outliers final: 45 residues processed: 397 average time/residue: 0.1253 time to fit residues: 78.9138 Evaluate side-chains 392 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 345 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 58 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 101 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 40 optimal weight: 0.0470 chunk 89 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN D 464 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124794 restraints weight = 28458.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127710 restraints weight = 15692.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129569 restraints weight = 10859.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130312 restraints weight = 8664.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131213 restraints weight = 7776.018| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19484 Z= 0.129 Angle : 0.728 12.307 26440 Z= 0.351 Chirality : 0.042 0.264 3012 Planarity : 0.004 0.051 3336 Dihedral : 4.676 28.139 2596 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.52 % Allowed : 21.46 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2356 helix: 1.11 (0.14), residues: 1364 sheet: -2.88 (0.53), residues: 56 loop : -2.31 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 224 TYR 0.026 0.001 TYR A 324 PHE 0.016 0.001 PHE B 478 TRP 0.009 0.001 TRP C 593 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00289 (19484) covalent geometry : angle 0.72756 (26440) hydrogen bonds : bond 0.03265 ( 884) hydrogen bonds : angle 3.91032 ( 2532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3566.53 seconds wall clock time: 62 minutes 17.23 seconds (3737.23 seconds total)