Starting phenix.real_space_refine on Tue Sep 15 10:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm6_30402/09_2026/7cm6_30402.cif" } resolution = 3.0 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 184 5.16 5 C 24384 2.51 5 N 6960 2.21 5 O 7136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38680 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 7.40, per 1000 atoms: 0.19 Number of scatterers: 38680 At special positions: 0 Unit cell: (214.165, 214.165, 82.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 16 15.00 O 7136 8.00 N 6960 7.00 C 24384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 8 sheets defined 70.0% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.550A pdb=" N LEU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.941A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.794A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.543A pdb=" N HIS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.553A pdb=" N LEU A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.661A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 338 through 359 removed outlier: 3.541A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.639A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.647A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.523A pdb=" N SER A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.723A pdb=" N VAL A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL A 675 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 677 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 678' Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR A 691 " --> pdb=" O TYR A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 86 through 104 removed outlier: 3.550A pdb=" N LEU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.941A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.196A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.543A pdb=" N HIS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.923A pdb=" N GLN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.660A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 338 through 359 removed outlier: 3.542A pdb=" N GLN B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.640A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.647A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.524A pdb=" N SER B 507 " --> pdb=" O TYR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 678 " --> pdb=" O VAL B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 678' Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR B 691 " --> pdb=" O TYR B 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 82 removed outlier: 3.519A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.550A pdb=" N LEU C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.660A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 338 through 359 removed outlier: 3.541A pdb=" N GLN C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.639A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 424 " --> pdb=" O TRP C 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.648A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 453 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 507 removed outlier: 3.524A pdb=" N SER C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 545 removed outlier: 3.936A pdb=" N MET C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL C 675 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 676 " --> pdb=" O GLN C 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 677 " --> pdb=" O ALA C 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 678 " --> pdb=" O VAL C 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 672 through 678' Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.548A pdb=" N THR C 691 " --> pdb=" O TYR C 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.550A pdb=" N LEU D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.558A pdb=" N LEU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 150 removed outlier: 3.941A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 Processing helix chain 'D' and resid 295 through 302 removed outlier: 3.860A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 3.660A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.541A pdb=" N GLN D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.640A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 424 " --> pdb=" O TRP D 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 425 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 removed outlier: 3.648A pdb=" N GLU D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 453 Processing helix chain 'D' and resid 459 through 476 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 507 removed outlier: 3.523A pdb=" N SER D 507 " --> pdb=" O TYR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.723A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 Processing helix chain 'D' and resid 607 through 614 Processing helix chain 'D' and resid 637 through 650 Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL D 675 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 676 " --> pdb=" O GLN D 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 677 " --> pdb=" O ALA D 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 678 " --> pdb=" O VAL D 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 672 through 678' Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR D 691 " --> pdb=" O TYR D 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.550A pdb=" N LEU E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.554A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 248 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER E 260 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.553A pdb=" N LEU E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 295 through 302 removed outlier: 3.860A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 312 removed outlier: 3.660A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 338 through 359 removed outlier: 3.541A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 369 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.640A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 425 " --> pdb=" O LEU E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.647A pdb=" N GLU E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 453 Processing helix chain 'E' and resid 459 through 476 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 507 removed outlier: 3.523A pdb=" N SER E 507 " --> pdb=" O TYR E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 586 Processing helix chain 'E' and resid 607 through 614 Processing helix chain 'E' and resid 637 through 650 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.715A pdb=" N VAL E 675 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E 676 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR E 677 " --> pdb=" O ALA E 674 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE E 678 " --> pdb=" O VAL E 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 672 through 678' Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.550A pdb=" N THR E 691 " --> pdb=" O TYR E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 86 through 104 removed outlier: 3.551A pdb=" N LEU F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.558A pdb=" N LEU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 236 removed outlier: 3.545A pdb=" N HIS F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 248 " --> pdb=" O ARG F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER F 260 " --> pdb=" O PRO F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU F 268 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 312 removed outlier: 3.660A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 338 through 359 removed outlier: 3.541A pdb=" N GLN F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 369 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.640A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 424 " --> pdb=" O TRP F 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY F 425 " --> pdb=" O LEU F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 3.647A pdb=" N GLU F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 453 Processing helix chain 'F' and resid 459 through 476 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.676A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 507 removed outlier: 3.524A pdb=" N SER F 507 " --> pdb=" O TYR F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 586 Processing helix chain 'F' and resid 607 through 614 Processing helix chain 'F' and resid 637 through 650 Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL F 675 " --> pdb=" O MET F 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 676 " --> pdb=" O GLN F 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 677 " --> pdb=" O ALA F 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 678 " --> pdb=" O VAL F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 672 through 678' Processing helix chain 'F' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR F 691 " --> pdb=" O TYR F 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 86 through 104 removed outlier: 3.550A pdb=" N LEU G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.943A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.925A pdb=" N GLN G 242 " --> pdb=" O GLY G 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER G 260 " --> pdb=" O PRO G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU G 268 " --> pdb=" O GLU G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'G' and resid 295 through 302 removed outlier: 3.860A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 removed outlier: 3.660A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 328 Processing helix chain 'G' and resid 338 through 359 removed outlier: 3.542A pdb=" N GLN G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 369 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 removed outlier: 3.576A pdb=" N SER G 387 " --> pdb=" O ASN G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.640A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 424 " --> pdb=" O TRP G 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY G 425 " --> pdb=" O LEU G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 435 removed outlier: 3.647A pdb=" N GLU G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 453 Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 507 removed outlier: 3.523A pdb=" N SER G 507 " --> pdb=" O TYR G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 586 Processing helix chain 'G' and resid 607 through 614 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL G 675 " --> pdb=" O MET G 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 676 " --> pdb=" O GLN G 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 677 " --> pdb=" O ALA G 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE G 678 " --> pdb=" O VAL G 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 672 through 678' Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.550A pdb=" N THR G 691 " --> pdb=" O TYR G 687 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 82 removed outlier: 3.520A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 86 through 104 removed outlier: 3.551A pdb=" N LEU H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN H 242 " --> pdb=" O GLY H 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS H 248 " --> pdb=" O ARG H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER H 260 " --> pdb=" O PRO H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 278 removed outlier: 3.553A pdb=" N LEU H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 291 Processing helix chain 'H' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 312 removed outlier: 3.661A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 328 Processing helix chain 'H' and resid 338 through 359 removed outlier: 3.540A pdb=" N GLN H 359 " --> pdb=" O ILE H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 369 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 removed outlier: 3.577A pdb=" N SER H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 removed outlier: 3.640A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE H 424 " --> pdb=" O TRP H 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 425 " --> pdb=" O LEU H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 435 removed outlier: 3.647A pdb=" N GLU H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 453 Processing helix chain 'H' and resid 459 through 476 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.676A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 507 removed outlier: 3.523A pdb=" N SER H 507 " --> pdb=" O TYR H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.723A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 586 Processing helix chain 'H' and resid 607 through 614 Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'H' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU H 676 " --> pdb=" O GLN H 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 677 " --> pdb=" O ALA H 674 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE H 678 " --> pdb=" O VAL H 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 672 through 678' Processing helix chain 'H' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR H 691 " --> pdb=" O TYR H 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.724A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.724A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) 1960 hydrogen bonds defined for protein. 5784 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: 8.62 Time building geometry restraints manager: 4.42 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: 8549 1.33 - 1.45: 7943 1.45 - 1.57: 22572 1.57 - 1.69: 24 1.69 - 1.81: 248 Bond restraints: 39336 Sorted by residual: bond pdb=" C2D NAD A1000 " pdb=" O2D NAD A1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C2D NAD D1000 " pdb=" O2D NAD D1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD B1000 " pdb=" O2D NAD B1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD H1000 " pdb=" O2D NAD H1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD G1000 " pdb=" O2D NAD G1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 39331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 52380 2.63 - 5.25: 675 5.25 - 7.88: 121 7.88 - 10.50: 32 10.50 - 13.13: 16 Bond angle restraints: 53224 Sorted by residual: angle pdb=" C SER F 336 " pdb=" N ASN F 337 " pdb=" CA ASN F 337 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" N VAL H 108 " pdb=" CA VAL H 108 " pdb=" C VAL H 108 " ideal model delta sigma weight residual 112.12 108.41 3.71 8.40e-01 1.42e+00 1.95e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N VAL B 108 " pdb=" CA VAL B 108 " pdb=" C VAL B 108 " ideal model delta sigma weight residual 112.12 108.42 3.70 8.40e-01 1.42e+00 1.94e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 ... (remaining 53219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 23006 15.00 - 30.00: 610 30.00 - 45.01: 136 45.01 - 60.01: 16 60.01 - 75.01: 16 Dihedral angle restraints: 23784 sinusoidal: 9736 harmonic: 14048 Sorted by residual: dihedral pdb=" CA TRP B 412 " pdb=" C TRP B 412 " pdb=" N LYS B 413 " pdb=" CA LYS B 413 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA TRP H 412 " pdb=" C TRP H 412 " pdb=" N LYS H 413 " pdb=" CA LYS H 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA TRP G 412 " pdb=" C TRP G 412 " pdb=" N LYS G 413 " pdb=" CA LYS G 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.93e+00 ... (remaining 23781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5433 0.069 - 0.138: 592 0.138 - 0.207: 36 0.207 - 0.276: 19 0.276 - 0.345: 8 Chirality restraints: 6088 Sorted by residual: chirality pdb=" C2D NAD D1000 " pdb=" C1D NAD D1000 " pdb=" C3D NAD D1000 " pdb=" O2D NAD D1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2D NAD F1000 " pdb=" C1D NAD F1000 " pdb=" C3D NAD F1000 " pdb=" O2D NAD F1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2D NAD H1000 " pdb=" C1D NAD H1000 " pdb=" C3D NAD H1000 " pdb=" O2D NAD H1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 6085 not shown) Planarity restraints: 6848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 283 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C VAL G 283 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL G 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU G 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C VAL F 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL F 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C VAL B 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL B 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 284 " 0.013 2.00e-02 2.50e+03 ... (remaining 6845 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10051 2.80 - 3.33: 33292 3.33 - 3.85: 61305 3.85 - 4.38: 72344 4.38 - 4.90: 124832 Nonbonded interactions: 301824 Sorted by model distance: nonbonded pdb=" OE1 GLN D 436 " pdb=" OG SER E 459 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLN A 436 " pdb=" OG SER B 459 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR B 568 " pdb=" OD1 ASP B 594 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR F 568 " pdb=" OD1 ASP F 594 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR A 568 " pdb=" OD1 ASP A 594 " model vdw 2.359 3.040 ... (remaining 301819 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 35.380 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.004 0.085 39336 Z= 0.217 Angle : 0.822 13.125 53224 Z= 0.435 Chirality : 0.047 0.345 6088 Planarity : 0.006 0.053 6848 Dihedral : 8.419 75.011 14664 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -4.13 (0.09), residues: 4824 helix: -2.88 (0.06), residues: 3184 sheet: -1.48 (0.42), residues: 136 loop : -2.00 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 121 TYR 0.010 0.001 TYR E 568 PHE 0.036 0.002 PHE D 192 TRP 0.016 0.002 TRP C 490 HIS 0.010 0.002 HIS G 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.22 (39336) covalent geometry : angle 0.82208 / 0.44 (53224) hydrogen bonds : bond 0.15012 / 9.99 ( 1960) hydrogen bonds : angle 6.38050 / 4.46 ( 5784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1045 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.6678 (tt) cc_final: 0.6456 (mp) REVERT: A 307 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6814 (ttp80) REVERT: A 638 TRP cc_start: 0.4921 (m100) cc_final: 0.4622 (m100) REVERT: A 672 MET cc_start: 0.3714 (ptm) cc_final: 0.3416 (ppp) REVERT: B 118 ASP cc_start: 0.6643 (m-30) cc_final: 0.6424 (m-30) REVERT: B 191 MET cc_start: 0.8527 (mmm) cc_final: 0.8215 (mmp) REVERT: B 638 TRP cc_start: 0.5266 (m100) cc_final: 0.4932 (m100) REVERT: C 307 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6667 (ttp80) REVERT: C 638 TRP cc_start: 0.4918 (m100) cc_final: 0.4501 (m100) REVERT: D 191 MET cc_start: 0.8640 (mmm) cc_final: 0.8428 (mmp) REVERT: D 638 TRP cc_start: 0.5379 (m100) cc_final: 0.5049 (m100) REVERT: E 191 MET cc_start: 0.8423 (mmm) cc_final: 0.8174 (mmp) REVERT: E 672 MET cc_start: 0.3662 (ptm) cc_final: 0.3401 (ppp) REVERT: F 638 TRP cc_start: 0.5395 (m100) cc_final: 0.5093 (m100) REVERT: G 638 TRP cc_start: 0.4926 (m100) cc_final: 0.4503 (m100) REVERT: G 672 MET cc_start: 0.3436 (ptm) cc_final: 0.3132 (ptm) REVERT: H 118 ASP cc_start: 0.6612 (m-30) cc_final: 0.6310 (m-30) REVERT: H 191 MET cc_start: 0.8516 (mmm) cc_final: 0.8210 (mmp) REVERT: H 638 TRP cc_start: 0.5274 (m100) cc_final: 0.4820 (m100) outliers start: 0 outliers final: 8 residues processed: 1045 average time/residue: 0.9380 time to fit residues: 1146.1965 Evaluate side-chains 410 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 402 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 134 GLN A 236 HIS A 239 GLN A 280 ASN A 575 GLN A 652 ASN B 114 GLN B 134 GLN B 170 ASN B 236 HIS B 280 ASN B 585 GLN B 652 ASN C 134 GLN C 236 HIS C 652 ASN D 134 GLN D 236 HIS D 652 ASN E 134 GLN E 236 HIS E 616 ASN E 652 ASN F 134 GLN F 236 HIS F 616 ASN F 652 ASN G 134 GLN G 236 HIS G 280 ASN G 575 GLN G 616 ASN G 652 ASN G 700 GLN H 114 GLN H 134 GLN H 236 HIS H 280 ASN H 585 GLN H 616 ASN H 652 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122195 restraints weight = 54507.616| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.53 r_work: 0.3040 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 39336 Z= 0.187 Angle : 0.610 8.415 53224 Z= 0.311 Chirality : 0.041 0.146 6088 Planarity : 0.005 0.054 6848 Dihedral : 6.555 166.954 5371 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.06 % Allowed : 10.76 % Favored : 86.18 % 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: -1.58 (0.11), residues: 4824 helix: -0.84 (0.08), residues: 3328 sheet: -1.62 (0.42), residues: 144 loop : -1.04 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 338 TYR 0.018 0.003 TYR G 687 PHE 0.031 0.003 PHE B 433 TRP 0.017 0.002 TRP E 412 HIS 0.007 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (39336) covalent geometry : angle 0.60973 / 0.31 (53224) hydrogen bonds : bond 0.04166 / 2.76 ( 1960) hydrogen bonds : angle 3.79286 / 2.68 ( 5784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 419 time to evaluate : 1.315 Fit side-chains REVERT: A 259 PHE cc_start: 0.8540 (t80) cc_final: 0.8202 (t80) REVERT: A 326 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: A 363 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7518 (tppp) REVERT: A 570 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5288 (mmt90) REVERT: A 672 MET cc_start: 0.4084 (ptm) cc_final: 0.3760 (ppp) REVERT: B 98 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7291 (mp) REVERT: B 545 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5731 (ppp) REVERT: B 638 TRP cc_start: 0.5734 (m100) cc_final: 0.5255 (m100) REVERT: C 326 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: C 363 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7501 (tppp) REVERT: C 672 MET cc_start: 0.3998 (ptm) cc_final: 0.3796 (ppp) REVERT: D 146 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7674 (ttt-90) REVERT: D 363 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7388 (tppp) REVERT: D 545 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5810 (ppp) REVERT: D 638 TRP cc_start: 0.5698 (m100) cc_final: 0.5192 (m100) REVERT: D 693 GLU cc_start: 0.7448 (tp30) cc_final: 0.6927 (tp30) REVERT: E 147 LEU cc_start: 0.8373 (tp) cc_final: 0.8049 (tt) REVERT: E 159 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7782 (tpp-160) REVERT: E 176 GLU cc_start: 0.7684 (mp0) cc_final: 0.7123 (tp30) REVERT: E 641 LYS cc_start: 0.6506 (mttm) cc_final: 0.6242 (tmtt) REVERT: E 672 MET cc_start: 0.4086 (ptm) cc_final: 0.3545 (ppp) REVERT: F 363 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7444 (tppp) REVERT: F 545 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5790 (ppp) REVERT: F 638 TRP cc_start: 0.5699 (m100) cc_final: 0.5249 (m100) REVERT: G 147 LEU cc_start: 0.8405 (tp) cc_final: 0.8099 (tt) REVERT: G 259 PHE cc_start: 0.8206 (t80) cc_final: 0.7956 (t80) REVERT: G 327 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (mp) REVERT: G 638 TRP cc_start: 0.4790 (m100) cc_final: 0.4552 (m100) REVERT: G 672 MET cc_start: 0.4111 (ptm) cc_final: 0.3845 (ppp) REVERT: H 170 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8293 (t0) REVERT: H 245 MET cc_start: 0.8174 (mtp) cc_final: 0.7963 (mtp) REVERT: H 638 TRP cc_start: 0.5648 (m100) cc_final: 0.5176 (m100) outliers start: 125 outliers final: 44 residues processed: 514 average time/residue: 0.8677 time to fit residues: 523.7014 Evaluate side-chains 346 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain E residue 159 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 672 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 462 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 470 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 432 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 153 optimal weight: 0.0270 chunk 338 optimal weight: 7.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 280 ASN C 575 GLN C 609 GLN C 700 GLN D 62 GLN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 HIS F 62 GLN F 170 ASN G 700 GLN H 97 GLN H 700 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123288 restraints weight = 54346.882| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.52 r_work: 0.3056 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 39336 Z= 0.106 Angle : 0.488 9.170 53224 Z= 0.246 Chirality : 0.037 0.139 6088 Planarity : 0.003 0.038 6848 Dihedral : 4.448 46.992 5354 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 12.48 % Favored : 84.63 % 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: -0.32 (0.12), residues: 4824 helix: 0.10 (0.09), residues: 3336 sheet: -1.37 (0.44), residues: 144 loop : -0.51 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 249 TYR 0.010 0.001 TYR F 503 PHE 0.017 0.001 PHE H 476 TRP 0.007 0.001 TRP G 412 HIS 0.003 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (39336) covalent geometry : angle 0.48762 / 0.25 (53224) hydrogen bonds : bond 0.03180 / 2.12 ( 1960) hydrogen bonds : angle 3.40129 / 2.39 ( 5784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 352 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8462 (tm) cc_final: 0.8123 (tp) REVERT: A 363 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7541 (tppp) REVERT: A 570 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5302 (mmt90) REVERT: A 630 MET cc_start: 0.3804 (ttt) cc_final: 0.3425 (mtt) REVERT: A 672 MET cc_start: 0.4066 (ptm) cc_final: 0.3751 (ppp) REVERT: B 363 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7332 (tppp) REVERT: B 434 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8337 (ttt-90) REVERT: B 586 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 638 TRP cc_start: 0.5581 (m100) cc_final: 0.5186 (m100) REVERT: B 693 GLU cc_start: 0.7322 (tp30) cc_final: 0.6860 (tp30) REVERT: C 149 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 150 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: C 326 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: C 628 LYS cc_start: 0.4236 (mttt) cc_final: 0.3595 (mmtp) REVERT: C 630 MET cc_start: 0.3600 (mtp) cc_final: 0.2621 (mtt) REVERT: C 672 MET cc_start: 0.4143 (ptm) cc_final: 0.3923 (ppp) REVERT: D 363 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7322 (tppp) REVERT: D 434 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8316 (ttt-90) REVERT: D 545 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5686 (ppp) REVERT: D 638 TRP cc_start: 0.5641 (m100) cc_final: 0.5224 (m100) REVERT: D 693 GLU cc_start: 0.7391 (tp30) cc_final: 0.6974 (tp30) REVERT: E 147 LEU cc_start: 0.8367 (tp) cc_final: 0.8067 (tt) REVERT: E 176 GLU cc_start: 0.7694 (mp0) cc_final: 0.7120 (tp30) REVERT: E 570 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5347 (mmt90) REVERT: E 641 LYS cc_start: 0.6473 (mttm) cc_final: 0.6225 (tmtt) REVERT: E 672 MET cc_start: 0.3832 (ptm) cc_final: 0.3378 (ppp) REVERT: F 179 GLU cc_start: 0.7454 (mp0) cc_final: 0.7064 (mm-30) REVERT: F 245 MET cc_start: 0.8143 (mtp) cc_final: 0.7929 (mtp) REVERT: F 363 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7345 (tppp) REVERT: F 575 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: F 638 TRP cc_start: 0.5704 (m100) cc_final: 0.5331 (m100) REVERT: G 147 LEU cc_start: 0.8436 (tp) cc_final: 0.8136 (tt) REVERT: G 176 GLU cc_start: 0.7717 (mp0) cc_final: 0.7173 (tm-30) REVERT: G 259 PHE cc_start: 0.8316 (t80) cc_final: 0.8009 (t80) REVERT: G 352 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: G 609 GLN cc_start: 0.5908 (mp10) cc_final: 0.5092 (tp-100) REVERT: G 672 MET cc_start: 0.4040 (ptm) cc_final: 0.3802 (ppp) REVERT: H 170 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8295 (t0) REVERT: H 434 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8332 (ttt-90) REVERT: H 545 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5760 (ppp) REVERT: H 586 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8085 (mm) REVERT: H 638 TRP cc_start: 0.5577 (m100) cc_final: 0.5122 (m100) REVERT: H 657 ILE cc_start: 0.6979 (mp) cc_final: 0.6300 (tp) outliers start: 118 outliers final: 46 residues processed: 447 average time/residue: 0.7576 time to fit residues: 407.1689 Evaluate side-chains 335 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 570 ARG Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 450 optimal weight: 0.8980 chunk 366 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 421 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 242 optimal weight: 0.2980 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 280 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 280 ASN C 652 ASN C 700 GLN D 575 GLN D 700 GLN H 62 GLN H 134 GLN ** H 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120117 restraints weight = 54029.179| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.61 r_work: 0.2997 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39336 Z= 0.148 Angle : 0.528 7.524 53224 Z= 0.266 Chirality : 0.039 0.141 6088 Planarity : 0.004 0.040 6848 Dihedral : 4.509 49.224 5354 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.99 % Allowed : 13.73 % Favored : 83.28 % 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: 0.12 (0.12), residues: 4824 helix: 0.45 (0.09), residues: 3368 sheet: -1.37 (0.44), residues: 144 loop : -0.41 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.011 0.002 TYR C 380 PHE 0.015 0.002 PHE H 476 TRP 0.007 0.001 TRP E 214 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (39336) covalent geometry : angle 0.52850 / 0.27 (53224) hydrogen bonds : bond 0.03603 / 2.40 ( 1960) hydrogen bonds : angle 3.41708 / 2.41 ( 5784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 298 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8506 (tm) cc_final: 0.8262 (tp) REVERT: A 326 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 363 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7584 (tppp) REVERT: A 570 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5321 (mmt90) REVERT: A 630 MET cc_start: 0.3806 (ttt) cc_final: 0.3284 (mtt) REVERT: A 672 MET cc_start: 0.4085 (ptm) cc_final: 0.3764 (ppp) REVERT: B 434 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8372 (ttt-90) REVERT: B 545 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5895 (ppp) REVERT: B 586 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 638 TRP cc_start: 0.5618 (m100) cc_final: 0.5205 (m100) REVERT: B 693 GLU cc_start: 0.7369 (tp30) cc_final: 0.6994 (tp30) REVERT: C 147 LEU cc_start: 0.8440 (tm) cc_final: 0.8214 (tp) REVERT: C 149 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 150 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: C 326 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: C 363 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7537 (tppp) REVERT: C 628 LYS cc_start: 0.4350 (mttt) cc_final: 0.3665 (mmtp) REVERT: D 101 GLU cc_start: 0.7248 (mt-10) cc_final: 0.7010 (mt-10) REVERT: D 146 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7540 (ttt-90) REVERT: D 434 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8433 (ttt-90) REVERT: D 545 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.5928 (ppp) REVERT: D 638 TRP cc_start: 0.5572 (m100) cc_final: 0.5141 (m100) REVERT: D 693 GLU cc_start: 0.7376 (tp30) cc_final: 0.6904 (tp30) REVERT: E 147 LEU cc_start: 0.8451 (tp) cc_final: 0.8124 (tt) REVERT: E 149 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7390 (tm-30) REVERT: E 641 LYS cc_start: 0.6503 (mttm) cc_final: 0.6259 (tmtt) REVERT: E 672 MET cc_start: 0.3833 (ptm) cc_final: 0.3367 (ppp) REVERT: F 179 GLU cc_start: 0.7449 (mp0) cc_final: 0.7178 (mm-30) REVERT: F 245 MET cc_start: 0.8331 (mtp) cc_final: 0.8123 (mtp) REVERT: F 264 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7103 (pt0) REVERT: F 322 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7416 (ptp-170) REVERT: F 434 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8370 (ttt-90) REVERT: F 575 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: F 638 TRP cc_start: 0.5909 (m100) cc_final: 0.5582 (m100) REVERT: G 147 LEU cc_start: 0.8467 (tp) cc_final: 0.8142 (tt) REVERT: G 149 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7428 (tm-30) REVERT: G 259 PHE cc_start: 0.8499 (t80) cc_final: 0.8138 (t80) REVERT: G 352 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: G 672 MET cc_start: 0.4265 (ptm) cc_final: 0.4035 (ptp) REVERT: H 101 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6504 (mp0) REVERT: H 147 LEU cc_start: 0.8511 (tp) cc_final: 0.8307 (tt) REVERT: H 170 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8316 (t0) REVERT: H 245 MET cc_start: 0.8315 (mtp) cc_final: 0.8106 (mtp) REVERT: H 434 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8395 (ttt-90) REVERT: H 545 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5910 (ppp) REVERT: H 586 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8122 (mm) REVERT: H 609 GLN cc_start: 0.6497 (mp10) cc_final: 0.5485 (tp-100) REVERT: H 638 TRP cc_start: 0.5604 (m100) cc_final: 0.5134 (m100) outliers start: 122 outliers final: 66 residues processed: 394 average time/residue: 0.7456 time to fit residues: 355.2359 Evaluate side-chains 353 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 267 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 chunk 177 optimal weight: 0.0870 chunk 310 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 244 optimal weight: 10.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 575 GLN B 616 ASN B 700 GLN C 328 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN E 652 ASN E 700 GLN F 700 GLN G 269 HIS ** G 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114344 restraints weight = 54309.438| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.41 r_work: 0.3261 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39336 Z= 0.098 Angle : 0.469 7.514 53224 Z= 0.237 Chirality : 0.037 0.136 6088 Planarity : 0.003 0.039 6848 Dihedral : 4.262 49.320 5354 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.62 % Allowed : 14.56 % Favored : 82.82 % 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: 0.68 (0.13), residues: 4824 helix: 0.86 (0.09), residues: 3360 sheet: -1.19 (0.44), residues: 144 loop : -0.15 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.015 0.001 TYR A 687 PHE 0.011 0.001 PHE H 476 TRP 0.005 0.001 TRP A 253 HIS 0.002 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (39336) covalent geometry : angle 0.46938 / 0.24 (53224) hydrogen bonds : bond 0.02977 / 1.98 ( 1960) hydrogen bonds : angle 3.19983 / 2.25 ( 5784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 294 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8561 (tm) cc_final: 0.8305 (tp) REVERT: A 326 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: A 363 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7577 (tppp) REVERT: A 672 MET cc_start: 0.4036 (ptm) cc_final: 0.3732 (ppp) REVERT: A 700 GLN cc_start: 0.5336 (mt0) cc_final: 0.5045 (mm-40) REVERT: B 363 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7394 (tppp) REVERT: B 434 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8264 (ttt-90) REVERT: B 545 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5665 (ppp) REVERT: B 586 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 638 TRP cc_start: 0.5649 (m100) cc_final: 0.5238 (m100) REVERT: B 693 GLU cc_start: 0.7276 (tp30) cc_final: 0.6961 (tp30) REVERT: C 147 LEU cc_start: 0.8451 (tm) cc_final: 0.8206 (tp) REVERT: C 149 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7137 (tm-30) REVERT: C 150 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: C 325 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7258 (p0) REVERT: C 628 LYS cc_start: 0.4237 (mttt) cc_final: 0.3817 (mmtp) REVERT: D 146 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7594 (ttt-90) REVERT: D 434 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8305 (ttt-90) REVERT: D 586 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8242 (mm) REVERT: D 638 TRP cc_start: 0.5578 (m100) cc_final: 0.5173 (m100) REVERT: D 693 GLU cc_start: 0.7261 (tp30) cc_final: 0.6826 (tp30) REVERT: D 700 GLN cc_start: 0.5937 (mt0) cc_final: 0.5614 (mm-40) REVERT: E 147 LEU cc_start: 0.8455 (tp) cc_final: 0.8176 (tt) REVERT: E 149 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7390 (tm-30) REVERT: E 176 GLU cc_start: 0.7407 (mp0) cc_final: 0.7015 (tp30) REVERT: E 641 LYS cc_start: 0.6458 (mttm) cc_final: 0.6238 (tmtt) REVERT: E 672 MET cc_start: 0.3800 (ptm) cc_final: 0.3356 (ppp) REVERT: E 699 LEU cc_start: 0.6256 (mt) cc_final: 0.5940 (tp) REVERT: F 245 MET cc_start: 0.8156 (mtp) cc_final: 0.7908 (mtp) REVERT: F 322 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7149 (ptp-170) REVERT: F 363 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7387 (tppp) REVERT: F 434 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (ttt-90) REVERT: F 575 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6579 (pt0) REVERT: F 638 TRP cc_start: 0.5938 (m100) cc_final: 0.5617 (m100) REVERT: G 147 LEU cc_start: 0.8494 (tp) cc_final: 0.8216 (tt) REVERT: G 149 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7366 (tm-30) REVERT: G 176 GLU cc_start: 0.7516 (mp0) cc_final: 0.7088 (tp30) REVERT: G 700 GLN cc_start: 0.5013 (mt0) cc_final: 0.4528 (mm-40) REVERT: H 101 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6613 (mp0) REVERT: H 170 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.7974 (t160) REVERT: H 245 MET cc_start: 0.8158 (mtp) cc_final: 0.7898 (mtp) REVERT: H 586 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8143 (mm) REVERT: H 609 GLN cc_start: 0.6533 (mp10) cc_final: 0.5544 (tp-100) REVERT: H 638 TRP cc_start: 0.5598 (m100) cc_final: 0.5168 (m100) REVERT: H 657 ILE cc_start: 0.7035 (mp) cc_final: 0.6488 (tp) REVERT: H 700 GLN cc_start: 0.6070 (mt0) cc_final: 0.5544 (mm-40) outliers start: 107 outliers final: 56 residues processed: 380 average time/residue: 0.7131 time to fit residues: 329.3984 Evaluate side-chains 333 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 456 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 219 optimal weight: 0.0060 chunk 201 optimal weight: 0.7980 chunk 288 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 overall best weight: 1.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN B 280 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 328 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 585 GLN ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112573 restraints weight = 54429.528| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.43 r_work: 0.3232 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39336 Z= 0.121 Angle : 0.499 12.012 53224 Z= 0.249 Chirality : 0.038 0.152 6088 Planarity : 0.003 0.039 6848 Dihedral : 4.263 49.182 5354 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.16 % Allowed : 14.22 % Favored : 82.62 % 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: 0.83 (0.13), residues: 4824 helix: 0.94 (0.09), residues: 3392 sheet: -1.08 (0.45), residues: 144 loop : -0.02 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 307 TYR 0.010 0.001 TYR G 380 PHE 0.041 0.001 PHE G 259 TRP 0.006 0.001 TRP C 253 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (39336) covalent geometry : angle 0.49889 / 0.25 (53224) hydrogen bonds : bond 0.03253 / 2.16 ( 1960) hydrogen bonds : angle 3.23557 / 2.28 ( 5784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 284 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: A 363 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7596 (tppp) REVERT: A 672 MET cc_start: 0.3956 (ptm) cc_final: 0.3523 (ppp) REVERT: A 700 GLN cc_start: 0.5256 (mt0) cc_final: 0.4957 (mm-40) REVERT: B 322 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7327 (ptp-170) REVERT: B 545 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5708 (ppp) REVERT: B 586 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 638 TRP cc_start: 0.5657 (m100) cc_final: 0.5236 (m100) REVERT: B 700 GLN cc_start: 0.5961 (mt0) cc_final: 0.5533 (mm-40) REVERT: C 149 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 150 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: C 322 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7576 (ptp-170) REVERT: C 325 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7303 (p0) REVERT: C 363 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7628 (tppp) REVERT: D 434 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8321 (ttt-90) REVERT: D 545 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5746 (ppp) REVERT: D 638 TRP cc_start: 0.5581 (m100) cc_final: 0.5177 (m100) REVERT: D 693 GLU cc_start: 0.7252 (tp30) cc_final: 0.6829 (tp30) REVERT: E 147 LEU cc_start: 0.8464 (tp) cc_final: 0.8177 (tt) REVERT: E 149 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7274 (tm-30) REVERT: E 170 ASN cc_start: 0.8385 (t0) cc_final: 0.7910 (t160) REVERT: E 176 GLU cc_start: 0.7373 (mp0) cc_final: 0.7032 (tp30) REVERT: E 641 LYS cc_start: 0.6529 (mttm) cc_final: 0.6270 (tmtt) REVERT: E 672 MET cc_start: 0.3720 (ptm) cc_final: 0.3273 (ppp) REVERT: E 698 PHE cc_start: 0.6495 (m-80) cc_final: 0.6292 (m-10) REVERT: E 699 LEU cc_start: 0.6097 (mt) cc_final: 0.5791 (tp) REVERT: F 146 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7536 (ttp-170) REVERT: F 245 MET cc_start: 0.8238 (mtp) cc_final: 0.7977 (mtp) REVERT: F 322 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7265 (ptp-170) REVERT: F 363 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7387 (tppp) REVERT: F 434 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8300 (ttt-90) REVERT: F 575 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6693 (pt0) REVERT: F 638 TRP cc_start: 0.5990 (m100) cc_final: 0.5680 (m100) REVERT: G 147 LEU cc_start: 0.8493 (tp) cc_final: 0.8203 (tt) REVERT: G 149 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7301 (tm-30) REVERT: G 176 GLU cc_start: 0.7533 (mp0) cc_final: 0.7115 (tp30) REVERT: G 363 LYS cc_start: 0.7762 (tppp) cc_final: 0.7542 (tttp) REVERT: G 609 GLN cc_start: 0.5845 (mp10) cc_final: 0.5054 (tp-100) REVERT: G 700 GLN cc_start: 0.5053 (mt0) cc_final: 0.4659 (mm-40) REVERT: H 101 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6508 (mp0) REVERT: H 170 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7982 (t160) REVERT: H 245 MET cc_start: 0.8175 (mtp) cc_final: 0.7940 (mtp) REVERT: H 434 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8320 (ttt-90) REVERT: H 545 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5778 (ppp) REVERT: H 586 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8097 (mm) REVERT: H 638 TRP cc_start: 0.5608 (m100) cc_final: 0.5131 (m100) REVERT: H 657 ILE cc_start: 0.7069 (mp) cc_final: 0.6540 (tp) REVERT: H 700 GLN cc_start: 0.6189 (mt0) cc_final: 0.5720 (mm-40) outliers start: 129 outliers final: 70 residues processed: 383 average time/residue: 0.7408 time to fit residues: 343.3402 Evaluate side-chains 349 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 259 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 459 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 328 GLN E 134 GLN E 280 ASN E 616 ASN E 652 ASN F 134 GLN F 700 GLN G 62 GLN ** G 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113537 restraints weight = 54362.315| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.59 r_work: 0.3173 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39336 Z= 0.160 Angle : 0.543 10.913 53224 Z= 0.272 Chirality : 0.040 0.156 6088 Planarity : 0.004 0.039 6848 Dihedral : 4.442 51.134 5354 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.01 % Allowed : 14.44 % Favored : 82.55 % 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: 0.77 (0.13), residues: 4824 helix: 0.88 (0.09), residues: 3392 sheet: -1.33 (0.43), residues: 152 loop : 0.04 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 162 TYR 0.012 0.002 TYR B 380 PHE 0.012 0.002 PHE H 308 TRP 0.008 0.001 TRP E 638 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (39336) covalent geometry : angle 0.54257 / 0.27 (53224) hydrogen bonds : bond 0.03639 / 2.42 ( 1960) hydrogen bonds : angle 3.39041 / 2.39 ( 5784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 289 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8447 (tm) cc_final: 0.8210 (tp) REVERT: A 326 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 363 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7655 (tppp) REVERT: A 545 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.4926 (pmm) REVERT: A 672 MET cc_start: 0.3974 (ptm) cc_final: 0.3569 (ppp) REVERT: A 699 LEU cc_start: 0.6210 (mt) cc_final: 0.5975 (tp) REVERT: B 545 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5783 (ppp) REVERT: B 586 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (mm) REVERT: B 638 TRP cc_start: 0.5775 (m100) cc_final: 0.5362 (m100) REVERT: B 700 GLN cc_start: 0.6233 (mt0) cc_final: 0.5896 (mm-40) REVERT: C 149 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7284 (tm-30) REVERT: C 150 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: C 322 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7513 (ptp-170) REVERT: C 325 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 363 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7660 (tppp) REVERT: C 545 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4714 (pmm) REVERT: D 146 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7705 (ttt-90) REVERT: D 434 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8443 (ttt-90) REVERT: D 545 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5841 (ppp) REVERT: D 586 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (mm) REVERT: D 638 TRP cc_start: 0.5760 (m100) cc_final: 0.5321 (m100) REVERT: D 699 LEU cc_start: 0.6803 (mt) cc_final: 0.6509 (tp) REVERT: E 147 LEU cc_start: 0.8512 (tp) cc_final: 0.8185 (tt) REVERT: E 149 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 176 GLU cc_start: 0.7407 (mp0) cc_final: 0.7042 (tp30) REVERT: E 672 MET cc_start: 0.3834 (ptm) cc_final: 0.3446 (ppp) REVERT: F 146 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7750 (ttp-170) REVERT: F 245 MET cc_start: 0.8406 (mtp) cc_final: 0.8116 (mtp) REVERT: F 434 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8364 (ttt-90) REVERT: F 575 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: F 638 TRP cc_start: 0.6062 (m100) cc_final: 0.5755 (m100) REVERT: G 98 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7434 (tt) REVERT: G 101 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6812 (mp0) REVERT: G 147 LEU cc_start: 0.8564 (tp) cc_final: 0.8246 (tt) REVERT: G 149 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7405 (tm-30) REVERT: G 176 GLU cc_start: 0.7592 (mp0) cc_final: 0.7144 (tp30) REVERT: G 699 LEU cc_start: 0.6174 (mt) cc_final: 0.5883 (tp) REVERT: H 245 MET cc_start: 0.8351 (mtp) cc_final: 0.8107 (mtp) REVERT: H 322 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7292 (ptp-170) REVERT: H 434 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8394 (ttt-90) REVERT: H 545 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5915 (ppp) REVERT: H 586 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (mm) REVERT: H 638 TRP cc_start: 0.5637 (m100) cc_final: 0.5175 (m100) REVERT: H 700 GLN cc_start: 0.6113 (mt0) cc_final: 0.5886 (mm-40) outliers start: 123 outliers final: 70 residues processed: 383 average time/residue: 0.7440 time to fit residues: 344.5386 Evaluate side-chains 353 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 262 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 238 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 328 optimal weight: 0.5980 chunk 426 optimal weight: 5.9990 chunk 476 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN G 134 GLN G 328 GLN ** G 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** 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 = 0.3985 r_free = 0.3985 target = 0.152756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110331 restraints weight = 54084.853| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.43 r_work: 0.3195 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39336 Z= 0.175 Angle : 0.573 12.198 53224 Z= 0.287 Chirality : 0.040 0.174 6088 Planarity : 0.004 0.039 6848 Dihedral : 4.544 53.523 5354 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.94 % Allowed : 14.83 % Favored : 82.23 % 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: 0.68 (0.13), residues: 4824 helix: 0.78 (0.09), residues: 3424 sheet: -1.43 (0.43), residues: 152 loop : 0.09 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 249 TYR 0.016 0.002 TYR C 687 PHE 0.016 0.002 PHE H 308 TRP 0.010 0.001 TRP E 638 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 (39336) covalent geometry : angle 0.57347 / 0.29 (53224) hydrogen bonds : bond 0.03760 / 2.50 ( 1960) hydrogen bonds : angle 3.47470 / 2.44 ( 5784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 282 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.6830 (mtm110) cc_final: 0.6530 (tmm-80) REVERT: A 147 LEU cc_start: 0.8425 (tm) cc_final: 0.8179 (tp) REVERT: A 326 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: A 672 MET cc_start: 0.3991 (ptm) cc_final: 0.3541 (ppp) REVERT: A 699 LEU cc_start: 0.6300 (mt) cc_final: 0.6027 (tp) REVERT: B 545 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5663 (ppp) REVERT: B 638 TRP cc_start: 0.5770 (m100) cc_final: 0.5400 (m100) REVERT: B 700 GLN cc_start: 0.6382 (mt0) cc_final: 0.5988 (mm-40) REVERT: C 147 LEU cc_start: 0.8495 (tp) cc_final: 0.8115 (tt) REVERT: C 149 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7104 (tm-30) REVERT: C 150 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: D 146 ARG cc_start: 0.8050 (ttp-170) cc_final: 0.7744 (ttt-90) REVERT: D 434 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8349 (ttt-90) REVERT: D 545 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5673 (ppp) REVERT: D 586 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8070 (mm) REVERT: D 638 TRP cc_start: 0.5804 (m100) cc_final: 0.5420 (m100) REVERT: D 699 LEU cc_start: 0.6571 (mt) cc_final: 0.6358 (tp) REVERT: E 147 LEU cc_start: 0.8501 (tp) cc_final: 0.8175 (tt) REVERT: E 149 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7233 (tm-30) REVERT: E 170 ASN cc_start: 0.8439 (t0) cc_final: 0.7917 (t160) REVERT: E 176 GLU cc_start: 0.7402 (mp0) cc_final: 0.7034 (tp30) REVERT: E 545 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.4730 (pmm) REVERT: E 609 GLN cc_start: 0.5630 (mp10) cc_final: 0.5068 (tp-100) REVERT: E 672 MET cc_start: 0.3833 (ptm) cc_final: 0.3431 (ppp) REVERT: F 146 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7623 (ttp-170) REVERT: F 245 MET cc_start: 0.8420 (mtp) cc_final: 0.8118 (mtp) REVERT: F 434 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8273 (ttt-90) REVERT: F 575 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6701 (pt0) REVERT: F 638 TRP cc_start: 0.6411 (m100) cc_final: 0.6132 (m100) REVERT: G 101 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6768 (mp0) REVERT: G 147 LEU cc_start: 0.8525 (tp) cc_final: 0.8209 (tt) REVERT: G 149 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7289 (tm-30) REVERT: G 176 GLU cc_start: 0.7499 (mp0) cc_final: 0.7150 (tp30) REVERT: G 699 LEU cc_start: 0.6213 (mt) cc_final: 0.5925 (tp) REVERT: H 170 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8226 (t0) REVERT: H 245 MET cc_start: 0.8371 (mtp) cc_final: 0.8120 (mtp) REVERT: H 322 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7406 (ptp-170) REVERT: H 434 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8293 (ttt-90) REVERT: H 545 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5731 (ppp) REVERT: H 638 TRP cc_start: 0.5664 (m100) cc_final: 0.5253 (m100) outliers start: 120 outliers final: 66 residues processed: 371 average time/residue: 0.7021 time to fit residues: 313.5628 Evaluate side-chains 339 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 259 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 338 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 351 optimal weight: 0.7980 chunk 310 optimal weight: 0.3980 chunk 306 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN E 328 GLN ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN G 383 ASN G 700 GLN ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111062 restraints weight = 54266.533| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.51 r_work: 0.3225 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39336 Z= 0.108 Angle : 0.517 12.937 53224 Z= 0.258 Chirality : 0.038 0.148 6088 Planarity : 0.003 0.038 6848 Dihedral : 4.279 53.709 5352 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.43 % Allowed : 15.61 % Favored : 81.96 % 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: 1.06 (0.13), residues: 4824 helix: 1.09 (0.09), residues: 3424 sheet: -1.27 (0.43), residues: 152 loop : 0.14 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 249 TYR 0.011 0.001 TYR F 213 PHE 0.011 0.001 PHE H 308 TRP 0.007 0.001 TRP E 638 HIS 0.003 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (39336) covalent geometry : angle 0.51660 / 0.26 (53224) hydrogen bonds : bond 0.03044 / 2.02 ( 1960) hydrogen bonds : angle 3.26189 / 2.29 ( 5784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 299 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8407 (tm) cc_final: 0.8148 (tp) REVERT: A 326 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: A 672 MET cc_start: 0.3975 (ptm) cc_final: 0.3532 (ppp) REVERT: A 699 LEU cc_start: 0.6515 (mt) cc_final: 0.6264 (tp) REVERT: B 322 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7634 (ptp-170) REVERT: B 545 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5605 (ppp) REVERT: B 638 TRP cc_start: 0.5729 (m100) cc_final: 0.5352 (m100) REVERT: B 699 LEU cc_start: 0.6504 (mt) cc_final: 0.6269 (tp) REVERT: B 700 GLN cc_start: 0.6186 (mt0) cc_final: 0.5819 (mm-40) REVERT: C 146 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7680 (ttt-90) REVERT: C 147 LEU cc_start: 0.8444 (tp) cc_final: 0.8073 (tt) REVERT: C 149 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7122 (tm-30) REVERT: C 150 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: C 170 ASN cc_start: 0.8321 (t0) cc_final: 0.7745 (t160) REVERT: D 146 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7528 (ttt-90) REVERT: D 545 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5614 (ppp) REVERT: D 568 TYR cc_start: 0.7093 (p90) cc_final: 0.6710 (p90) REVERT: D 586 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7974 (mm) REVERT: D 638 TRP cc_start: 0.5770 (m100) cc_final: 0.5388 (m100) REVERT: E 147 LEU cc_start: 0.8464 (tp) cc_final: 0.8177 (tt) REVERT: E 170 ASN cc_start: 0.8421 (t0) cc_final: 0.7933 (t160) REVERT: E 176 GLU cc_start: 0.7401 (mp0) cc_final: 0.7043 (tp30) REVERT: E 545 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.4942 (pmm) REVERT: E 672 MET cc_start: 0.3824 (ptm) cc_final: 0.3452 (ppp) REVERT: F 245 MET cc_start: 0.8360 (mtp) cc_final: 0.8044 (mtp) REVERT: F 322 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7689 (ptp-170) REVERT: F 434 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8262 (ttt-90) REVERT: F 545 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5504 (ppp) REVERT: F 575 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6610 (pt0) REVERT: F 638 TRP cc_start: 0.6458 (m100) cc_final: 0.6180 (m100) REVERT: G 101 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6777 (mp0) REVERT: G 176 GLU cc_start: 0.7523 (mp0) cc_final: 0.7156 (tp30) REVERT: G 545 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.4884 (pmm) REVERT: G 609 GLN cc_start: 0.6043 (mp10) cc_final: 0.5329 (tp-100) REVERT: G 699 LEU cc_start: 0.6301 (mt) cc_final: 0.6004 (tp) REVERT: H 101 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6344 (mp0) REVERT: H 245 MET cc_start: 0.8363 (mtp) cc_final: 0.8096 (mtp) REVERT: H 434 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8278 (ttt-90) REVERT: H 545 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.5609 (ppp) REVERT: H 568 TYR cc_start: 0.7143 (p90) cc_final: 0.6823 (p90) REVERT: H 586 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (mm) REVERT: H 638 TRP cc_start: 0.5701 (m100) cc_final: 0.5316 (m100) REVERT: H 686 GLU cc_start: 0.7864 (mp0) cc_final: 0.6595 (pt0) REVERT: H 687 TYR cc_start: 0.7018 (m-80) cc_final: 0.6619 (m-10) outliers start: 99 outliers final: 58 residues processed: 373 average time/residue: 0.7068 time to fit residues: 322.2772 Evaluate side-chains 339 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 266 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 323 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 383 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN C 616 ASN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** H 700 GLN ** 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 = 0.3991 r_free = 0.3991 target = 0.153227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111072 restraints weight = 54141.474| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.44 r_work: 0.3202 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39336 Z= 0.151 Angle : 0.574 12.696 53224 Z= 0.285 Chirality : 0.040 0.146 6088 Planarity : 0.004 0.039 6848 Dihedral : 4.393 54.358 5352 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.18 % Allowed : 16.45 % Favored : 81.37 % 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: 0.98 (0.13), residues: 4824 helix: 1.02 (0.09), residues: 3424 sheet: -1.27 (0.43), residues: 152 loop : 0.16 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 249 TYR 0.019 0.002 TYR C 687 PHE 0.016 0.001 PHE H 308 TRP 0.010 0.001 TRP C 638 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (39336) covalent geometry : angle 0.57373 / 0.29 (53224) hydrogen bonds : bond 0.03522 / 2.34 ( 1960) hydrogen bonds : angle 3.39725 / 2.38 ( 5784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 265 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7379 (mp) cc_final: 0.7026 (mp) REVERT: A 147 LEU cc_start: 0.8431 (tm) cc_final: 0.8189 (tp) REVERT: A 326 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: A 672 MET cc_start: 0.4006 (ptm) cc_final: 0.3567 (ppp) REVERT: A 699 LEU cc_start: 0.6542 (mt) cc_final: 0.6277 (tp) REVERT: B 545 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5617 (ppp) REVERT: B 586 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8119 (mm) REVERT: B 638 TRP cc_start: 0.5735 (m100) cc_final: 0.5337 (m100) REVERT: B 700 GLN cc_start: 0.6040 (mt0) cc_final: 0.5693 (mm-40) REVERT: C 97 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: C 146 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7823 (ttt-90) REVERT: C 147 LEU cc_start: 0.8459 (tp) cc_final: 0.8103 (tt) REVERT: C 149 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 150 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: C 170 ASN cc_start: 0.8447 (t0) cc_final: 0.7851 (t160) REVERT: D 146 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7696 (ttt-90) REVERT: D 545 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5628 (ppp) REVERT: D 638 TRP cc_start: 0.5781 (m100) cc_final: 0.5409 (m100) REVERT: D 686 GLU cc_start: 0.7901 (mp0) cc_final: 0.6601 (pt0) REVERT: E 147 LEU cc_start: 0.8502 (tp) cc_final: 0.8186 (tt) REVERT: E 170 ASN cc_start: 0.8442 (t0) cc_final: 0.7920 (t160) REVERT: E 176 GLU cc_start: 0.7372 (mp0) cc_final: 0.7028 (tp30) REVERT: E 672 MET cc_start: 0.3829 (ptm) cc_final: 0.3449 (ppp) REVERT: F 245 MET cc_start: 0.8366 (mtp) cc_final: 0.8045 (mtp) REVERT: F 322 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7333 (ptp-170) REVERT: F 434 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8254 (ttt-90) REVERT: F 545 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5598 (ppp) REVERT: F 575 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: F 638 TRP cc_start: 0.6469 (m100) cc_final: 0.6104 (m100) REVERT: G 101 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6725 (mp0) REVERT: G 176 GLU cc_start: 0.7536 (mp0) cc_final: 0.7163 (tp30) REVERT: G 545 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.4658 (pmm) REVERT: G 699 LEU cc_start: 0.6345 (mt) cc_final: 0.6046 (tp) REVERT: H 245 MET cc_start: 0.8344 (mtp) cc_final: 0.8064 (mtp) REVERT: H 434 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8292 (ttt-90) REVERT: H 545 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5717 (ppp) REVERT: H 586 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7965 (mm) REVERT: H 638 TRP cc_start: 0.5694 (m100) cc_final: 0.5237 (m100) outliers start: 89 outliers final: 59 residues processed: 329 average time/residue: 0.7344 time to fit residues: 294.0178 Evaluate side-chains 327 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 672 MET Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 81 optimal weight: 0.8980 chunk 433 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 279 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 419 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN D 616 ASN D 652 ASN D 700 GLN ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112813 restraints weight = 54250.369| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.41 r_work: 0.3240 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39336 Z= 0.109 Angle : 0.530 13.339 53224 Z= 0.264 Chirality : 0.038 0.145 6088 Planarity : 0.003 0.038 6848 Dihedral : 4.242 54.698 5352 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.96 % Allowed : 16.64 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.26 (0.13), residues: 4824 helix: 1.23 (0.09), residues: 3424 sheet: -1.10 (0.44), residues: 152 loop : 0.23 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 249 TYR 0.011 0.001 TYR F 213 PHE 0.012 0.001 PHE H 308 TRP 0.008 0.001 TRP E 638 HIS 0.003 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (39336) covalent geometry : angle 0.52970 / 0.26 (53224) hydrogen bonds : bond 0.03002 / 2.00 ( 1960) hydrogen bonds : angle 3.23452 / 2.27 ( 5784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13508.16 seconds wall clock time: 230 minutes 40.06 seconds (13840.06 seconds total)