Starting phenix.real_space_refine on Sat Jul 4 09:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4c_22664/07_2026/7k4c_22664_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4c_22664/07_2026/7k4c_22664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4c_22664/07_2026/7k4c_22664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4c_22664/07_2026/7k4c_22664.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4c_22664/07_2026/7k4c_22664_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4c_22664/07_2026/7k4c_22664_neut.cif" } resolution = 3.78 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= 0.002 sd= 0.017 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Br 5 7.06 5 S 160 5.16 5 C 12782 2.51 5 N 3335 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "C" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "D" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'81F': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.29, per 1000 atoms: 0.22 Number of scatterers: 19744 At special positions: 0 Unit cell: (143.45, 143.45, 126.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 5 34.99 Ca 2 19.99 S 160 16.00 O 3460 8.00 N 3335 7.00 C 12782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 810.6 milliseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 59.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.560A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.587A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.729A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.919A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.730A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 removed outlier: 4.044A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.505A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 261 removed outlier: 4.017A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.554A pdb=" N ILE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.523A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.675A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.660A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 removed outlier: 3.707A pdb=" N ASP A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.455A pdb=" N ILE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 446 removed outlier: 3.780A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.759A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 487 removed outlier: 3.605A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 512 removed outlier: 3.628A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 498 " --> pdb=" O CYS A 494 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 removed outlier: 3.563A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.720A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 4.233A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.561A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.587A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.730A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.919A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.729A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 removed outlier: 4.046A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.505A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.017A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.554A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.522A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.674A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.659A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.707A pdb=" N ASP B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.456A pdb=" N ILE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 446 removed outlier: 3.779A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.760A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 487 removed outlier: 3.604A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 512 removed outlier: 3.628A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 498 " --> pdb=" O CYS B 494 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 566 removed outlier: 3.564A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 581 removed outlier: 3.720A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 608 removed outlier: 4.233A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.561A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.587A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.729A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.918A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.730A pdb=" N ALA C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.045A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.505A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.017A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.554A pdb=" N ILE C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.522A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.675A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.660A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.707A pdb=" N ASP C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 415 through 420 removed outlier: 4.456A pdb=" N ILE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 446 removed outlier: 3.780A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.760A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 removed outlier: 3.605A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 512 removed outlier: 3.629A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 498 " --> pdb=" O CYS C 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 566 removed outlier: 3.564A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.721A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 4.234A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.562A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.586A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.730A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.918A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.729A pdb=" N ALA D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 removed outlier: 4.045A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.506A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.018A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.555A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.522A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.674A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.660A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 removed outlier: 3.708A pdb=" N ASP D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 395 " --> pdb=" O VAL D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.456A pdb=" N ILE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 446 removed outlier: 3.780A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.759A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 487 removed outlier: 3.604A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 512 removed outlier: 3.628A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 498 " --> pdb=" O CYS D 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 566 removed outlier: 3.563A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 581 removed outlier: 3.721A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 4.233A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 112 removed outlier: 3.895A pdb=" N SER A 112 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 270 removed outlier: 7.059A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 112 removed outlier: 3.897A pdb=" N SER B 112 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 270 removed outlier: 7.058A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.896A pdb=" N SER C 112 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 265 through 270 removed outlier: 7.059A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 111 through 112 removed outlier: 3.896A pdb=" N SER D 112 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 265 through 270 removed outlier: 7.059A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6705 1.37 - 1.51: 6918 1.51 - 1.66: 6309 1.66 - 1.80: 210 1.80 - 1.94: 67 Bond restraints: 20209 Sorted by residual: bond pdb=" C21 81F D 701 " pdb=" C22 81F D 701 " ideal model delta sigma weight residual 1.385 1.526 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C21 81F C 701 " pdb=" C22 81F C 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F B 701 " pdb=" C22 81F B 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F A 701 " pdb=" C22 81F A 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F D 702 " pdb=" C22 81F D 702 " ideal model delta sigma weight residual 1.385 1.515 -0.130 2.00e-02 2.50e+03 4.26e+01 ... (remaining 20204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 26237 2.35 - 4.69: 1010 4.69 - 7.04: 131 7.04 - 9.38: 42 9.38 - 11.73: 4 Bond angle restraints: 27424 Sorted by residual: angle pdb=" C TYR C 89 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C TYR D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C TYR A 89 " pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLN B 369 " pdb=" N GLN B 370 " pdb=" CA GLN B 370 " ideal model delta sigma weight residual 122.44 117.00 5.44 1.19e+00 7.06e-01 2.09e+01 ... (remaining 27419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 11326 16.96 - 33.91: 627 33.91 - 50.87: 139 50.87 - 67.82: 3 67.82 - 84.78: 38 Dihedral angle restraints: 12133 sinusoidal: 4985 harmonic: 7148 Sorted by residual: dihedral pdb=" CA SER A 112 " pdb=" C SER A 112 " pdb=" N GLU A 113 " pdb=" CA GLU A 113 " ideal model delta harmonic sigma weight residual 180.00 145.08 34.92 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA SER D 112 " pdb=" C SER D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual 180.00 145.14 34.86 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 12130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1993 0.051 - 0.102: 875 0.102 - 0.153: 193 0.153 - 0.204: 30 0.204 - 0.255: 11 Chirality restraints: 3102 Sorted by residual: chirality pdb=" C05 81F D 702 " pdb=" C04 81F D 702 " pdb=" C06 81F D 702 " pdb=" C08 81F D 702 " both_signs ideal model delta sigma weight residual False -2.52 -2.77 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C10 81F D 702 " pdb=" C07 81F D 702 " pdb=" C09 81F D 702 " pdb=" N01 81F D 702 " both_signs ideal model delta sigma weight residual False 2.33 2.58 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3099 not shown) Planarity restraints: 3454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 476 " -0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A 477 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO C 477 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO B 477 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " -0.046 5.00e-02 4.00e+02 ... (remaining 3451 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5973 2.82 - 3.34: 19219 3.34 - 3.86: 30411 3.86 - 4.38: 35228 4.38 - 4.90: 56514 Nonbonded interactions: 147345 Sorted by model distance: nonbonded pdb=" OH TYR C 339 " pdb=" O THR C 392 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 339 " pdb=" O THR B 392 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 204 " pdb=" ND2 ASN A 252 " model vdw 2.347 3.120 ... (remaining 147340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 28 through 701) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 28 through 701) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.860 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.009 0.141 20209 Z= 0.431 Angle : 1.088 11.728 27424 Z= 0.579 Chirality : 0.058 0.255 3102 Planarity : 0.007 0.084 3454 Dihedral : 12.364 84.777 7517 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.37 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.34 (0.12), residues: 2436 helix: -3.53 (0.08), residues: 1304 sheet: -3.43 (0.51), residues: 68 loop : -3.45 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 385 TYR 0.025 0.003 TYR D 623 PHE 0.029 0.003 PHE A 468 TRP 0.022 0.003 TRP C 613 HIS 0.012 0.002 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00926 / 0.43 (20209) covalent geometry : angle 1.08836 / 0.58 (27424) hydrogen bonds : bond 0.30745 / 20.09 ( 760) hydrogen bonds : angle 8.92258 / 6.34 ( 2220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9600 (pp) cc_final: 0.9014 (pp) REVERT: A 96 MET cc_start: 0.9311 (mmm) cc_final: 0.8681 (mmm) REVERT: A 99 MET cc_start: 0.9029 (mmp) cc_final: 0.8829 (mtp) REVERT: A 122 HIS cc_start: 0.9389 (m90) cc_final: 0.8575 (m90) REVERT: A 267 GLN cc_start: 0.8339 (tt0) cc_final: 0.8101 (tp40) REVERT: A 303 GLU cc_start: 0.8739 (tt0) cc_final: 0.8200 (tp30) REVERT: A 305 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7415 (mtt180) REVERT: A 332 LEU cc_start: 0.9399 (tp) cc_final: 0.9127 (tt) REVERT: A 383 ASP cc_start: 0.9169 (t0) cc_final: 0.8737 (m-30) REVERT: A 402 VAL cc_start: 0.9265 (p) cc_final: 0.8575 (p) REVERT: A 435 MET cc_start: 0.8824 (mmt) cc_final: 0.8011 (mmm) REVERT: A 440 MET cc_start: 0.8875 (tpt) cc_final: 0.8594 (tpp) REVERT: A 442 MET cc_start: 0.9316 (tpp) cc_final: 0.8623 (tpp) REVERT: A 444 LEU cc_start: 0.9467 (mp) cc_final: 0.9172 (mt) REVERT: A 515 GLU cc_start: 0.7496 (tp30) cc_final: 0.7265 (mm-30) REVERT: A 587 HIS cc_start: 0.8857 (p-80) cc_final: 0.8201 (p-80) REVERT: A 588 GLU cc_start: 0.9061 (tt0) cc_final: 0.8781 (tt0) REVERT: A 590 ASP cc_start: 0.8562 (m-30) cc_final: 0.8078 (p0) REVERT: A 603 MET cc_start: 0.8829 (ttt) cc_final: 0.8475 (tmm) REVERT: B 92 LEU cc_start: 0.9615 (pp) cc_final: 0.9053 (pp) REVERT: B 96 MET cc_start: 0.9300 (mmm) cc_final: 0.8679 (mmm) REVERT: B 122 HIS cc_start: 0.9377 (m90) cc_final: 0.8590 (m90) REVERT: B 127 ASN cc_start: 0.9231 (t160) cc_final: 0.9028 (m-40) REVERT: B 267 GLN cc_start: 0.8383 (tt0) cc_final: 0.8114 (tp40) REVERT: B 303 GLU cc_start: 0.8772 (tt0) cc_final: 0.8136 (tm-30) REVERT: B 332 LEU cc_start: 0.9323 (tp) cc_final: 0.9036 (tt) REVERT: B 383 ASP cc_start: 0.9158 (t0) cc_final: 0.8710 (m-30) REVERT: B 386 LEU cc_start: 0.9376 (tp) cc_final: 0.9139 (mm) REVERT: B 402 VAL cc_start: 0.9293 (p) cc_final: 0.8688 (p) REVERT: B 435 MET cc_start: 0.8786 (mmt) cc_final: 0.8041 (mmt) REVERT: B 436 VAL cc_start: 0.9484 (t) cc_final: 0.9120 (p) REVERT: B 440 MET cc_start: 0.8793 (tpt) cc_final: 0.8503 (tpp) REVERT: B 441 VAL cc_start: 0.9659 (t) cc_final: 0.9411 (t) REVERT: B 442 MET cc_start: 0.9352 (tpp) cc_final: 0.8682 (tpp) REVERT: B 444 LEU cc_start: 0.9487 (mp) cc_final: 0.9182 (mt) REVERT: B 587 HIS cc_start: 0.8910 (p-80) cc_final: 0.8597 (p-80) REVERT: B 588 GLU cc_start: 0.9060 (tt0) cc_final: 0.8752 (tt0) REVERT: C 92 LEU cc_start: 0.9621 (pp) cc_final: 0.9060 (pp) REVERT: C 96 MET cc_start: 0.9303 (mmm) cc_final: 0.8721 (mmm) REVERT: C 122 HIS cc_start: 0.9387 (m90) cc_final: 0.8612 (m90) REVERT: C 127 ASN cc_start: 0.9220 (t160) cc_final: 0.8949 (m-40) REVERT: C 178 ILE cc_start: 0.9529 (mp) cc_final: 0.9255 (mp) REVERT: C 260 MET cc_start: 0.8946 (tpp) cc_final: 0.8742 (tpp) REVERT: C 279 ASP cc_start: 0.8888 (t70) cc_final: 0.8536 (t0) REVERT: C 303 GLU cc_start: 0.8771 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 305 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8324 (ttm-80) REVERT: C 323 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8489 (mmt180) REVERT: C 332 LEU cc_start: 0.9330 (tp) cc_final: 0.9030 (tt) REVERT: C 386 LEU cc_start: 0.9343 (tp) cc_final: 0.9117 (mm) REVERT: C 402 VAL cc_start: 0.9246 (p) cc_final: 0.8670 (p) REVERT: C 435 MET cc_start: 0.8890 (mmt) cc_final: 0.8296 (mmt) REVERT: C 440 MET cc_start: 0.8731 (tpt) cc_final: 0.8520 (tpp) REVERT: C 442 MET cc_start: 0.9342 (tpp) cc_final: 0.8745 (tpp) REVERT: C 485 MET cc_start: 0.8504 (ttm) cc_final: 0.7927 (ttm) REVERT: C 587 HIS cc_start: 0.8918 (p-80) cc_final: 0.8623 (p-80) REVERT: C 588 GLU cc_start: 0.9054 (tt0) cc_final: 0.8742 (tt0) REVERT: D 66 LYS cc_start: 0.9473 (tppt) cc_final: 0.9048 (tptp) REVERT: D 92 LEU cc_start: 0.9632 (pp) cc_final: 0.8956 (pp) REVERT: D 96 MET cc_start: 0.9254 (mmm) cc_final: 0.8532 (mmm) REVERT: D 99 MET cc_start: 0.8975 (mmp) cc_final: 0.8686 (mtt) REVERT: D 157 CYS cc_start: 0.9382 (m) cc_final: 0.8949 (t) REVERT: D 178 ILE cc_start: 0.9464 (mp) cc_final: 0.9206 (mp) REVERT: D 213 CYS cc_start: 0.9025 (t) cc_final: 0.8407 (t) REVERT: D 255 MET cc_start: 0.8702 (tpp) cc_final: 0.8185 (tpt) REVERT: D 274 THR cc_start: 0.8698 (m) cc_final: 0.8352 (m) REVERT: D 305 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7310 (mtt180) REVERT: D 318 SER cc_start: 0.9724 (t) cc_final: 0.9497 (p) REVERT: D 330 CYS cc_start: 0.9587 (m) cc_final: 0.9320 (m) REVERT: D 332 LEU cc_start: 0.9393 (tp) cc_final: 0.9105 (tt) REVERT: D 435 MET cc_start: 0.8879 (mmt) cc_final: 0.8201 (mmm) REVERT: D 440 MET cc_start: 0.8959 (tpt) cc_final: 0.8686 (tpp) REVERT: D 442 MET cc_start: 0.9396 (tpp) cc_final: 0.8729 (tpp) REVERT: D 444 LEU cc_start: 0.9523 (mp) cc_final: 0.9190 (mt) REVERT: D 452 VAL cc_start: 0.9460 (t) cc_final: 0.9229 (t) REVERT: D 456 PHE cc_start: 0.9186 (m-10) cc_final: 0.8718 (m-10) REVERT: D 485 MET cc_start: 0.8481 (ttm) cc_final: 0.7458 (ttm) REVERT: D 587 HIS cc_start: 0.8875 (p-80) cc_final: 0.8476 (p-80) REVERT: D 588 GLU cc_start: 0.8961 (tt0) cc_final: 0.8389 (tm-30) REVERT: D 590 ASP cc_start: 0.8673 (m-30) cc_final: 0.8359 (p0) REVERT: D 603 MET cc_start: 0.8816 (ttt) cc_final: 0.8565 (tmm) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.1428 time to fit residues: 129.5484 Evaluate side-chains 376 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 197 ASN A 258 HIS A 464 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 118 GLN B 127 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN C 74 GLN C 118 GLN C 127 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN D 74 GLN D 197 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.099517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077765 restraints weight = 55523.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080910 restraints weight = 26766.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083069 restraints weight = 16416.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084512 restraints weight = 11618.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085627 restraints weight = 9106.355| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20209 Z= 0.147 Angle : 0.749 10.333 27424 Z= 0.380 Chirality : 0.042 0.151 3102 Planarity : 0.005 0.070 3454 Dihedral : 9.551 89.866 2805 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.08 % Allowed : 13.02 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.65 (0.15), residues: 2436 helix: -1.81 (0.12), residues: 1392 sheet: -3.04 (0.54), residues: 68 loop : -3.22 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 302 TYR 0.033 0.002 TYR C 324 PHE 0.018 0.001 PHE D 162 TRP 0.010 0.001 TRP D 321 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (20209) covalent geometry : angle 0.74890 / 0.38 (27424) hydrogen bonds : bond 0.05066 / 3.31 ( 760) hydrogen bonds : angle 5.29645 / 3.83 ( 2220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 439 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9435 (pp) cc_final: 0.8994 (pt) REVERT: A 96 MET cc_start: 0.9090 (mmm) cc_final: 0.8550 (mmp) REVERT: A 122 HIS cc_start: 0.9438 (m90) cc_final: 0.8706 (m90) REVERT: A 345 MET cc_start: 0.8702 (tpp) cc_final: 0.8354 (tpp) REVERT: A 383 ASP cc_start: 0.9093 (t0) cc_final: 0.8622 (m-30) REVERT: A 435 MET cc_start: 0.8882 (mmt) cc_final: 0.8071 (mmm) REVERT: A 444 LEU cc_start: 0.9572 (mp) cc_final: 0.9211 (mt) REVERT: A 466 MET cc_start: 0.9426 (mtt) cc_final: 0.9145 (mmt) REVERT: A 515 GLU cc_start: 0.7567 (tp30) cc_final: 0.7120 (mm-30) REVERT: A 554 MET cc_start: 0.8451 (tpt) cc_final: 0.8202 (tpt) REVERT: A 578 MET cc_start: 0.8090 (mmt) cc_final: 0.7889 (mmt) REVERT: A 587 HIS cc_start: 0.8901 (p-80) cc_final: 0.8236 (p-80) REVERT: A 588 GLU cc_start: 0.9026 (tt0) cc_final: 0.8819 (tt0) REVERT: A 590 ASP cc_start: 0.8656 (m-30) cc_final: 0.8112 (p0) REVERT: A 635 ASP cc_start: 0.8659 (t0) cc_final: 0.8318 (t0) REVERT: B 92 LEU cc_start: 0.9450 (pp) cc_final: 0.9086 (pt) REVERT: B 122 HIS cc_start: 0.9454 (m90) cc_final: 0.8750 (m90) REVERT: B 132 LEU cc_start: 0.9139 (mt) cc_final: 0.8922 (mt) REVERT: B 200 LEU cc_start: 0.9436 (mt) cc_final: 0.9193 (mt) REVERT: B 267 GLN cc_start: 0.8378 (tt0) cc_final: 0.8154 (tp-100) REVERT: B 318 SER cc_start: 0.9788 (t) cc_final: 0.9549 (p) REVERT: B 383 ASP cc_start: 0.9088 (t0) cc_final: 0.8603 (m-30) REVERT: B 435 MET cc_start: 0.8920 (mmt) cc_final: 0.8112 (mmm) REVERT: B 442 MET cc_start: 0.9065 (tpp) cc_final: 0.8837 (mmm) REVERT: B 444 LEU cc_start: 0.9552 (mp) cc_final: 0.9201 (mt) REVERT: B 485 MET cc_start: 0.8239 (ttm) cc_final: 0.7378 (ttm) REVERT: B 515 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7450 (mp0) REVERT: B 554 MET cc_start: 0.8604 (tpt) cc_final: 0.8275 (tpt) REVERT: B 577 MET cc_start: 0.8741 (tpp) cc_final: 0.8378 (tpp) REVERT: B 587 HIS cc_start: 0.8915 (p-80) cc_final: 0.8271 (p-80) REVERT: B 590 ASP cc_start: 0.8711 (m-30) cc_final: 0.8085 (p0) REVERT: C 92 LEU cc_start: 0.9465 (pp) cc_final: 0.9085 (pt) REVERT: C 122 HIS cc_start: 0.9429 (m90) cc_final: 0.8698 (m90) REVERT: C 159 LEU cc_start: 0.9444 (tp) cc_final: 0.9133 (tt) REVERT: C 267 GLN cc_start: 0.8317 (tt0) cc_final: 0.8116 (tp-100) REVERT: C 318 SER cc_start: 0.9771 (t) cc_final: 0.9519 (p) REVERT: C 383 ASP cc_start: 0.9097 (t0) cc_final: 0.8647 (m-30) REVERT: C 435 MET cc_start: 0.8956 (mmt) cc_final: 0.8094 (mmt) REVERT: C 442 MET cc_start: 0.9130 (tpp) cc_final: 0.8538 (tpp) REVERT: C 515 GLU cc_start: 0.7598 (tp30) cc_final: 0.7334 (mm-30) REVERT: C 528 MET cc_start: 0.8647 (tpp) cc_final: 0.8355 (tpp) REVERT: C 587 HIS cc_start: 0.8916 (p-80) cc_final: 0.8266 (p-80) REVERT: C 590 ASP cc_start: 0.8707 (m-30) cc_final: 0.8063 (p0) REVERT: D 29 TRP cc_start: 0.6790 (t-100) cc_final: 0.6379 (t60) REVERT: D 66 LYS cc_start: 0.9486 (tppt) cc_final: 0.9011 (tptp) REVERT: D 92 LEU cc_start: 0.9468 (pp) cc_final: 0.9018 (pt) REVERT: D 96 MET cc_start: 0.9023 (mmm) cc_final: 0.8402 (mmp) REVERT: D 122 HIS cc_start: 0.9509 (m90) cc_final: 0.8898 (m90) REVERT: D 137 LEU cc_start: 0.9727 (mp) cc_final: 0.9491 (pp) REVERT: D 178 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.8918 (mm) REVERT: D 315 GLU cc_start: 0.9180 (tp30) cc_final: 0.8682 (tp30) REVERT: D 318 SER cc_start: 0.9745 (t) cc_final: 0.9454 (p) REVERT: D 383 ASP cc_start: 0.9057 (t0) cc_final: 0.8497 (m-30) REVERT: D 435 MET cc_start: 0.8842 (mmt) cc_final: 0.8017 (mmt) REVERT: D 440 MET cc_start: 0.9073 (tpt) cc_final: 0.8866 (tpp) REVERT: D 444 LEU cc_start: 0.9566 (mp) cc_final: 0.9236 (mt) REVERT: D 466 MET cc_start: 0.9412 (mtt) cc_final: 0.8981 (mmt) REVERT: D 485 MET cc_start: 0.8140 (ttm) cc_final: 0.7779 (ttm) REVERT: D 528 MET cc_start: 0.8745 (tpp) cc_final: 0.8542 (tpp) REVERT: D 554 MET cc_start: 0.8579 (tpt) cc_final: 0.8293 (tpt) REVERT: D 587 HIS cc_start: 0.8891 (p-80) cc_final: 0.8550 (p-80) REVERT: D 588 GLU cc_start: 0.8889 (tt0) cc_final: 0.8353 (tm-30) REVERT: D 590 ASP cc_start: 0.8699 (m-30) cc_final: 0.8237 (p0) REVERT: D 603 MET cc_start: 0.8793 (ttt) cc_final: 0.8513 (tmm) outliers start: 44 outliers final: 20 residues processed: 461 average time/residue: 0.1248 time to fit residues: 91.9334 Evaluate side-chains 386 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 365 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 546 ASN B 197 ASN B 464 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** 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 = 0.3722 r_free = 0.3722 target = 0.099769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077542 restraints weight = 55178.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.080722 restraints weight = 26796.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082950 restraints weight = 16523.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084463 restraints weight = 11722.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085456 restraints weight = 9196.736| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20209 Z= 0.128 Angle : 0.693 11.475 27424 Z= 0.345 Chirality : 0.041 0.147 3102 Planarity : 0.004 0.067 3454 Dihedral : 9.456 89.426 2805 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.02 % Allowed : 14.15 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2436 helix: -0.87 (0.13), residues: 1336 sheet: -3.03 (0.55), residues: 68 loop : -3.01 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 584 TYR 0.023 0.001 TYR C 324 PHE 0.021 0.001 PHE D 162 TRP 0.008 0.001 TRP C 613 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (20209) covalent geometry : angle 0.69275 / 0.35 (27424) hydrogen bonds : bond 0.03968 / 2.60 ( 760) hydrogen bonds : angle 4.78124 / 3.46 ( 2220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 395 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9475 (pp) cc_final: 0.9166 (pp) REVERT: A 96 MET cc_start: 0.8994 (mmm) cc_final: 0.8718 (mmp) REVERT: A 99 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8536 (ptp) REVERT: A 122 HIS cc_start: 0.9357 (m90) cc_final: 0.8648 (m90) REVERT: A 290 GLN cc_start: 0.8359 (pp30) cc_final: 0.7894 (pp30) REVERT: A 302 ARG cc_start: 0.8225 (tpm170) cc_final: 0.7520 (tpm170) REVERT: A 383 ASP cc_start: 0.9029 (t0) cc_final: 0.8604 (m-30) REVERT: A 444 LEU cc_start: 0.9506 (mp) cc_final: 0.9273 (mt) REVERT: A 466 MET cc_start: 0.9359 (mtt) cc_final: 0.9151 (mmt) REVERT: A 474 MET cc_start: 0.8758 (tpp) cc_final: 0.8536 (tpp) REVERT: A 515 GLU cc_start: 0.7346 (tp30) cc_final: 0.6835 (mm-30) REVERT: A 528 MET cc_start: 0.8377 (tpp) cc_final: 0.8096 (tpp) REVERT: A 587 HIS cc_start: 0.8794 (p-80) cc_final: 0.8307 (p-80) REVERT: A 590 ASP cc_start: 0.8573 (m-30) cc_final: 0.7993 (p0) REVERT: A 635 ASP cc_start: 0.8592 (t0) cc_final: 0.8177 (t0) REVERT: B 92 LEU cc_start: 0.9457 (pp) cc_final: 0.9174 (pp) REVERT: B 122 HIS cc_start: 0.9355 (m90) cc_final: 0.8659 (m90) REVERT: B 159 LEU cc_start: 0.9422 (tp) cc_final: 0.9125 (tt) REVERT: B 200 LEU cc_start: 0.9381 (mt) cc_final: 0.9136 (mt) REVERT: B 302 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.7613 (tpp-160) REVERT: B 318 SER cc_start: 0.9786 (t) cc_final: 0.9541 (p) REVERT: B 383 ASP cc_start: 0.9026 (t0) cc_final: 0.8546 (m-30) REVERT: B 440 MET cc_start: 0.9272 (tpp) cc_final: 0.9063 (tpp) REVERT: B 442 MET cc_start: 0.9089 (tpp) cc_final: 0.8835 (mmm) REVERT: B 444 LEU cc_start: 0.9493 (mp) cc_final: 0.9247 (mt) REVERT: B 474 MET cc_start: 0.8727 (tpp) cc_final: 0.8482 (tpp) REVERT: B 485 MET cc_start: 0.8119 (ttm) cc_final: 0.7466 (ttm) REVERT: B 515 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7397 (mp0) REVERT: B 528 MET cc_start: 0.8538 (tpp) cc_final: 0.8283 (tpp) REVERT: B 554 MET cc_start: 0.8322 (tpt) cc_final: 0.8082 (tpt) REVERT: B 577 MET cc_start: 0.8624 (tpp) cc_final: 0.8354 (tpp) REVERT: B 578 MET cc_start: 0.8104 (mmt) cc_final: 0.7796 (mmt) REVERT: B 587 HIS cc_start: 0.8807 (p-80) cc_final: 0.8302 (p-80) REVERT: B 590 ASP cc_start: 0.8670 (m-30) cc_final: 0.8012 (p0) REVERT: B 635 ASP cc_start: 0.8607 (t0) cc_final: 0.8193 (t0) REVERT: C 122 HIS cc_start: 0.9331 (m90) cc_final: 0.8632 (m90) REVERT: C 318 SER cc_start: 0.9772 (t) cc_final: 0.9521 (p) REVERT: C 383 ASP cc_start: 0.9058 (t0) cc_final: 0.8532 (m-30) REVERT: C 435 MET cc_start: 0.9047 (mmt) cc_final: 0.8155 (mmt) REVERT: C 442 MET cc_start: 0.9174 (tpp) cc_final: 0.8816 (mmm) REVERT: C 515 GLU cc_start: 0.7570 (tp30) cc_final: 0.7323 (mm-30) REVERT: C 528 MET cc_start: 0.8603 (tpp) cc_final: 0.8324 (tpp) REVERT: C 578 MET cc_start: 0.8139 (mmt) cc_final: 0.7623 (mmt) REVERT: C 587 HIS cc_start: 0.8836 (p-80) cc_final: 0.8285 (p-80) REVERT: C 590 ASP cc_start: 0.8693 (m-30) cc_final: 0.8039 (p0) REVERT: D 29 TRP cc_start: 0.6805 (t-100) cc_final: 0.6415 (t60) REVERT: D 66 LYS cc_start: 0.9484 (tppt) cc_final: 0.9010 (tptp) REVERT: D 92 LEU cc_start: 0.9430 (pp) cc_final: 0.9124 (pt) REVERT: D 122 HIS cc_start: 0.9445 (m90) cc_final: 0.8827 (m90) REVERT: D 177 GLU cc_start: 0.9113 (pm20) cc_final: 0.8907 (pm20) REVERT: D 178 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8685 (mm) REVERT: D 315 GLU cc_start: 0.9160 (tp30) cc_final: 0.8676 (tp30) REVERT: D 318 SER cc_start: 0.9751 (t) cc_final: 0.9462 (p) REVERT: D 331 MET cc_start: 0.8491 (tpp) cc_final: 0.7768 (tmm) REVERT: D 383 ASP cc_start: 0.8975 (t0) cc_final: 0.8448 (m-30) REVERT: D 402 VAL cc_start: 0.9091 (p) cc_final: 0.8347 (p) REVERT: D 435 MET cc_start: 0.8900 (mmt) cc_final: 0.8095 (mmt) REVERT: D 440 MET cc_start: 0.9054 (tpt) cc_final: 0.8808 (tpp) REVERT: D 444 LEU cc_start: 0.9569 (mp) cc_final: 0.9242 (mt) REVERT: D 466 MET cc_start: 0.9324 (mtt) cc_final: 0.8983 (mmt) REVERT: D 485 MET cc_start: 0.8141 (ttm) cc_final: 0.7927 (ttm) REVERT: D 528 MET cc_start: 0.8712 (tpp) cc_final: 0.8414 (tpp) REVERT: D 554 MET cc_start: 0.8543 (tpt) cc_final: 0.8127 (tpt) REVERT: D 578 MET cc_start: 0.8269 (mmt) cc_final: 0.7890 (mmt) REVERT: D 587 HIS cc_start: 0.8764 (p-80) cc_final: 0.8458 (p-80) REVERT: D 590 ASP cc_start: 0.8631 (m-30) cc_final: 0.8143 (p0) REVERT: D 603 MET cc_start: 0.8776 (ttt) cc_final: 0.8457 (tmm) REVERT: D 635 ASP cc_start: 0.8535 (t0) cc_final: 0.8163 (t0) outliers start: 64 outliers final: 30 residues processed: 438 average time/residue: 0.1259 time to fit residues: 90.2691 Evaluate side-chains 383 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 351 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 134 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.096019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073798 restraints weight = 55182.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076880 restraints weight = 27097.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079003 restraints weight = 16823.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080383 restraints weight = 11997.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081417 restraints weight = 9515.033| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20209 Z= 0.198 Angle : 0.754 11.533 27424 Z= 0.374 Chirality : 0.043 0.158 3102 Planarity : 0.005 0.058 3454 Dihedral : 9.648 89.802 2805 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.35 % Allowed : 16.37 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.17), residues: 2436 helix: -0.58 (0.13), residues: 1400 sheet: -2.91 (0.57), residues: 68 loop : -2.97 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 584 TYR 0.018 0.002 TYR C 324 PHE 0.013 0.001 PHE C 162 TRP 0.011 0.001 TRP A 593 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (20209) covalent geometry : angle 0.75413 / 0.37 (27424) hydrogen bonds : bond 0.03714 / 2.45 ( 760) hydrogen bonds : angle 4.76977 / 3.45 ( 2220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 369 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.9356 (m-30) cc_final: 0.9139 (m-30) REVERT: A 92 LEU cc_start: 0.9574 (pp) cc_final: 0.9104 (pp) REVERT: A 122 HIS cc_start: 0.9325 (m90) cc_final: 0.8671 (m90) REVERT: A 125 VAL cc_start: 0.9573 (t) cc_final: 0.9363 (p) REVERT: A 176 GLU cc_start: 0.9353 (pm20) cc_final: 0.8996 (pm20) REVERT: A 200 LEU cc_start: 0.9329 (mt) cc_final: 0.9109 (mt) REVERT: A 302 ARG cc_start: 0.8248 (tpm170) cc_final: 0.7501 (tpm170) REVERT: A 383 ASP cc_start: 0.9068 (t0) cc_final: 0.8563 (m-30) REVERT: A 435 MET cc_start: 0.9001 (mmt) cc_final: 0.8055 (mmm) REVERT: A 444 LEU cc_start: 0.9501 (mp) cc_final: 0.9249 (mt) REVERT: A 466 MET cc_start: 0.9423 (mtt) cc_final: 0.9164 (mmt) REVERT: A 515 GLU cc_start: 0.7359 (tp30) cc_final: 0.6817 (mm-30) REVERT: A 577 MET cc_start: 0.8745 (tpp) cc_final: 0.8456 (tpp) REVERT: A 635 ASP cc_start: 0.8592 (t0) cc_final: 0.8295 (t0) REVERT: B 122 HIS cc_start: 0.9310 (m90) cc_final: 0.8641 (m90) REVERT: B 159 LEU cc_start: 0.9419 (tp) cc_final: 0.9085 (tt) REVERT: B 200 LEU cc_start: 0.9394 (mt) cc_final: 0.9193 (mt) REVERT: B 242 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9042 (t) REVERT: B 318 SER cc_start: 0.9804 (t) cc_final: 0.9549 (p) REVERT: B 331 MET cc_start: 0.8476 (tpp) cc_final: 0.7666 (tmm) REVERT: B 383 ASP cc_start: 0.9046 (t0) cc_final: 0.8560 (m-30) REVERT: B 435 MET cc_start: 0.9052 (mmt) cc_final: 0.8148 (mmm) REVERT: B 442 MET cc_start: 0.9044 (tpp) cc_final: 0.8782 (mmm) REVERT: B 554 MET cc_start: 0.8503 (tpt) cc_final: 0.8244 (tpt) REVERT: B 577 MET cc_start: 0.8702 (tpp) cc_final: 0.8339 (tpp) REVERT: B 578 MET cc_start: 0.8058 (mmt) cc_final: 0.7750 (mmt) REVERT: B 635 ASP cc_start: 0.8595 (t0) cc_final: 0.8300 (t0) REVERT: C 122 HIS cc_start: 0.9296 (m90) cc_final: 0.8638 (m90) REVERT: C 159 LEU cc_start: 0.9437 (tp) cc_final: 0.9126 (tt) REVERT: C 176 GLU cc_start: 0.9334 (pm20) cc_final: 0.9096 (mp0) REVERT: C 178 ILE cc_start: 0.9643 (mp) cc_final: 0.9245 (mp) REVERT: C 215 MET cc_start: 0.8813 (mmt) cc_final: 0.8574 (mmp) REVERT: C 281 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8656 (p) REVERT: C 318 SER cc_start: 0.9796 (t) cc_final: 0.9539 (p) REVERT: C 383 ASP cc_start: 0.9053 (t0) cc_final: 0.8610 (m-30) REVERT: C 435 MET cc_start: 0.9027 (mmt) cc_final: 0.8188 (mmm) REVERT: C 442 MET cc_start: 0.9145 (tpp) cc_final: 0.8790 (mmm) REVERT: C 515 GLU cc_start: 0.7648 (tp30) cc_final: 0.7239 (mm-30) REVERT: C 528 MET cc_start: 0.8782 (tpp) cc_final: 0.8468 (tpp) REVERT: C 577 MET cc_start: 0.8753 (tpp) cc_final: 0.8390 (tpp) REVERT: C 578 MET cc_start: 0.8115 (mmt) cc_final: 0.7773 (mmt) REVERT: C 635 ASP cc_start: 0.8495 (t0) cc_final: 0.8164 (t0) REVERT: D 66 LYS cc_start: 0.9500 (tppt) cc_final: 0.9028 (tptp) REVERT: D 92 LEU cc_start: 0.9351 (pp) cc_final: 0.9072 (pp) REVERT: D 125 VAL cc_start: 0.9557 (t) cc_final: 0.9342 (p) REVERT: D 177 GLU cc_start: 0.9192 (pm20) cc_final: 0.8933 (pm20) REVERT: D 178 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8705 (mm) REVERT: D 318 SER cc_start: 0.9782 (t) cc_final: 0.9508 (p) REVERT: D 331 MET cc_start: 0.8556 (tpp) cc_final: 0.7816 (tmm) REVERT: D 383 ASP cc_start: 0.8961 (t0) cc_final: 0.8424 (m-30) REVERT: D 435 MET cc_start: 0.8949 (mmt) cc_final: 0.8003 (mmm) REVERT: D 440 MET cc_start: 0.9177 (tpt) cc_final: 0.8919 (tpp) REVERT: D 444 LEU cc_start: 0.9578 (mp) cc_final: 0.9274 (mt) REVERT: D 445 ILE cc_start: 0.9596 (tp) cc_final: 0.9337 (pt) REVERT: D 466 MET cc_start: 0.9319 (mtt) cc_final: 0.9003 (mmt) REVERT: D 485 MET cc_start: 0.8178 (ttm) cc_final: 0.7832 (ttm) REVERT: D 528 MET cc_start: 0.8841 (tpp) cc_final: 0.8588 (tpp) REVERT: D 554 MET cc_start: 0.8428 (tpt) cc_final: 0.8133 (tpt) REVERT: D 577 MET cc_start: 0.8532 (tpp) cc_final: 0.8323 (tpp) REVERT: D 578 MET cc_start: 0.8121 (mmt) cc_final: 0.7895 (mmt) REVERT: D 603 MET cc_start: 0.8855 (ttt) cc_final: 0.8507 (tmm) REVERT: D 635 ASP cc_start: 0.8614 (t0) cc_final: 0.8284 (t0) outliers start: 71 outliers final: 38 residues processed: 411 average time/residue: 0.1193 time to fit residues: 81.0967 Evaluate side-chains 384 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 343 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 94 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 231 optimal weight: 0.0570 chunk 78 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 201 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078166 restraints weight = 53762.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081382 restraints weight = 26105.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083590 restraints weight = 16012.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085079 restraints weight = 11298.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086165 restraints weight = 8824.942| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20209 Z= 0.116 Angle : 0.719 13.080 27424 Z= 0.345 Chirality : 0.042 0.166 3102 Planarity : 0.004 0.063 3454 Dihedral : 9.092 89.937 2805 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.31 % Allowed : 18.49 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.17), residues: 2436 helix: -0.23 (0.14), residues: 1376 sheet: -2.80 (0.59), residues: 68 loop : -2.89 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 75 TYR 0.022 0.001 TYR C 324 PHE 0.012 0.001 PHE A 211 TRP 0.009 0.001 TRP C 613 HIS 0.006 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20209) covalent geometry : angle 0.71908 / 0.35 (27424) hydrogen bonds : bond 0.03179 / 2.08 ( 760) hydrogen bonds : angle 4.25277 / 3.09 ( 2220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6837 (t-100) cc_final: 0.6463 (t60) REVERT: A 44 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9109 (tt) REVERT: A 92 LEU cc_start: 0.9527 (pp) cc_final: 0.9320 (pt) REVERT: A 122 HIS cc_start: 0.9329 (m90) cc_final: 0.8640 (m90) REVERT: A 125 VAL cc_start: 0.9486 (t) cc_final: 0.9264 (p) REVERT: A 200 LEU cc_start: 0.9229 (mt) cc_final: 0.8749 (mt) REVERT: A 290 GLN cc_start: 0.8533 (pm20) cc_final: 0.8094 (mm-40) REVERT: A 331 MET cc_start: 0.8529 (tpp) cc_final: 0.7583 (tmm) REVERT: A 383 ASP cc_start: 0.9045 (t0) cc_final: 0.8577 (m-30) REVERT: A 435 MET cc_start: 0.8861 (mmt) cc_final: 0.7875 (mmm) REVERT: A 444 LEU cc_start: 0.9533 (mp) cc_final: 0.9320 (mt) REVERT: A 466 MET cc_start: 0.9439 (mtt) cc_final: 0.9164 (mmt) REVERT: A 515 GLU cc_start: 0.7362 (tp30) cc_final: 0.6931 (mm-30) REVERT: A 577 MET cc_start: 0.8638 (tpp) cc_final: 0.8343 (tpp) REVERT: A 635 ASP cc_start: 0.8560 (t0) cc_final: 0.8317 (t0) REVERT: B 122 HIS cc_start: 0.9298 (m90) cc_final: 0.8606 (m90) REVERT: B 125 VAL cc_start: 0.9531 (t) cc_final: 0.9316 (p) REVERT: B 176 GLU cc_start: 0.9420 (pm20) cc_final: 0.9008 (mp0) REVERT: B 200 LEU cc_start: 0.9290 (mt) cc_final: 0.8795 (mt) REVERT: B 232 LEU cc_start: 0.8545 (tt) cc_final: 0.8211 (tp) REVERT: B 242 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8941 (t) REVERT: B 290 GLN cc_start: 0.8536 (pm20) cc_final: 0.7773 (mm-40) REVERT: B 302 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7341 (tpm170) REVERT: B 318 SER cc_start: 0.9792 (t) cc_final: 0.9540 (p) REVERT: B 331 MET cc_start: 0.8457 (tpp) cc_final: 0.7631 (tmm) REVERT: B 383 ASP cc_start: 0.9043 (t0) cc_final: 0.8558 (m-30) REVERT: B 435 MET cc_start: 0.8863 (mmt) cc_final: 0.7926 (mmm) REVERT: B 440 MET cc_start: 0.9380 (tpp) cc_final: 0.9086 (tmm) REVERT: B 442 MET cc_start: 0.9027 (tpp) cc_final: 0.8790 (mmm) REVERT: B 515 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 554 MET cc_start: 0.8407 (tpt) cc_final: 0.8120 (tpt) REVERT: B 577 MET cc_start: 0.8600 (tpp) cc_final: 0.8269 (tpp) REVERT: B 635 ASP cc_start: 0.8567 (t0) cc_final: 0.8265 (t0) REVERT: C 44 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9262 (mp) REVERT: C 51 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8316 (mt) REVERT: C 122 HIS cc_start: 0.9307 (m90) cc_final: 0.8586 (m90) REVERT: C 125 VAL cc_start: 0.9636 (t) cc_final: 0.9396 (p) REVERT: C 173 VAL cc_start: 0.8596 (t) cc_final: 0.8375 (p) REVERT: C 176 GLU cc_start: 0.9463 (pm20) cc_final: 0.8978 (mp0) REVERT: C 177 GLU cc_start: 0.9184 (pm20) cc_final: 0.8709 (pm20) REVERT: C 178 ILE cc_start: 0.9511 (mp) cc_final: 0.9015 (mp) REVERT: C 215 MET cc_start: 0.8900 (mmt) cc_final: 0.8511 (mmp) REVERT: C 259 LEU cc_start: 0.9121 (tp) cc_final: 0.8857 (tt) REVERT: C 290 GLN cc_start: 0.8618 (pm20) cc_final: 0.7851 (mm-40) REVERT: C 302 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7517 (tpp-160) REVERT: C 318 SER cc_start: 0.9771 (t) cc_final: 0.9518 (p) REVERT: C 383 ASP cc_start: 0.9021 (t0) cc_final: 0.8503 (m-30) REVERT: C 435 MET cc_start: 0.8930 (mmt) cc_final: 0.8050 (mmm) REVERT: C 442 MET cc_start: 0.9071 (tpp) cc_final: 0.8773 (mmm) REVERT: C 515 GLU cc_start: 0.7434 (tp30) cc_final: 0.7046 (mm-30) REVERT: C 528 MET cc_start: 0.8585 (tpp) cc_final: 0.8204 (tpp) REVERT: C 577 MET cc_start: 0.8678 (tpp) cc_final: 0.8434 (tpp) REVERT: C 635 ASP cc_start: 0.8457 (t0) cc_final: 0.8141 (t0) REVERT: D 29 TRP cc_start: 0.6824 (t-100) cc_final: 0.6426 (t60) REVERT: D 66 LYS cc_start: 0.9502 (tppt) cc_final: 0.9042 (tptp) REVERT: D 96 MET cc_start: 0.9387 (ptt) cc_final: 0.8983 (ptp) REVERT: D 99 MET cc_start: 0.8967 (mpp) cc_final: 0.8614 (ptp) REVERT: D 100 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8426 (mm-30) REVERT: D 177 GLU cc_start: 0.9228 (pm20) cc_final: 0.8943 (pm20) REVERT: D 178 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.8767 (mm) REVERT: D 290 GLN cc_start: 0.8657 (pm20) cc_final: 0.7861 (mm-40) REVERT: D 315 GLU cc_start: 0.9212 (tp30) cc_final: 0.8742 (tp30) REVERT: D 318 SER cc_start: 0.9757 (t) cc_final: 0.9472 (p) REVERT: D 331 MET cc_start: 0.8510 (tpp) cc_final: 0.7763 (tmm) REVERT: D 383 ASP cc_start: 0.8921 (t0) cc_final: 0.8412 (m-30) REVERT: D 435 MET cc_start: 0.8767 (mmt) cc_final: 0.7910 (mmt) REVERT: D 440 MET cc_start: 0.9207 (tpt) cc_final: 0.8922 (tmm) REVERT: D 445 ILE cc_start: 0.9611 (tp) cc_final: 0.9333 (pt) REVERT: D 466 MET cc_start: 0.9334 (mtt) cc_final: 0.9003 (mmt) REVERT: D 474 MET cc_start: 0.8771 (tpp) cc_final: 0.8568 (tpp) REVERT: D 485 MET cc_start: 0.8198 (ttm) cc_final: 0.7646 (ttm) REVERT: D 528 MET cc_start: 0.8674 (tpp) cc_final: 0.8320 (tpp) REVERT: D 554 MET cc_start: 0.8326 (tpt) cc_final: 0.8042 (tpt) REVERT: D 603 MET cc_start: 0.8771 (ttt) cc_final: 0.8473 (tmm) REVERT: D 635 ASP cc_start: 0.8506 (t0) cc_final: 0.8206 (t0) outliers start: 49 outliers final: 31 residues processed: 412 average time/residue: 0.1246 time to fit residues: 83.3564 Evaluate side-chains 383 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 197 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.098170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076181 restraints weight = 53834.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079320 restraints weight = 26559.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081487 restraints weight = 16375.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082938 restraints weight = 11610.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084009 restraints weight = 9124.624| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20209 Z= 0.139 Angle : 0.723 12.740 27424 Z= 0.349 Chirality : 0.042 0.160 3102 Planarity : 0.004 0.054 3454 Dihedral : 8.629 88.307 2805 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.78 % Allowed : 19.34 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.82 (0.17), residues: 2436 helix: -0.03 (0.14), residues: 1368 sheet: -2.87 (0.59), residues: 68 loop : -2.81 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 75 TYR 0.021 0.001 TYR C 324 PHE 0.009 0.001 PHE D 468 TRP 0.008 0.001 TRP A 593 HIS 0.006 0.001 HIS C 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (20209) covalent geometry : angle 0.72287 / 0.35 (27424) hydrogen bonds : bond 0.03169 / 2.08 ( 760) hydrogen bonds : angle 4.29014 / 3.12 ( 2220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 357 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 HIS cc_start: 0.9313 (m90) cc_final: 0.8855 (m-70) REVERT: A 176 GLU cc_start: 0.9433 (pm20) cc_final: 0.8979 (pm20) REVERT: A 200 LEU cc_start: 0.9267 (mt) cc_final: 0.8784 (mt) REVERT: A 290 GLN cc_start: 0.8497 (pm20) cc_final: 0.8077 (mm-40) REVERT: A 302 ARG cc_start: 0.8273 (tpm170) cc_final: 0.8029 (tpm170) REVERT: A 331 MET cc_start: 0.8536 (tpp) cc_final: 0.7613 (tmm) REVERT: A 383 ASP cc_start: 0.9057 (t0) cc_final: 0.8590 (m-30) REVERT: A 435 MET cc_start: 0.8953 (mmt) cc_final: 0.7970 (mmm) REVERT: A 466 MET cc_start: 0.9416 (mtt) cc_final: 0.9165 (mmt) REVERT: A 515 GLU cc_start: 0.7383 (tp30) cc_final: 0.6922 (mm-30) REVERT: A 577 MET cc_start: 0.8627 (tpp) cc_final: 0.8301 (tpp) REVERT: A 635 ASP cc_start: 0.8605 (t0) cc_final: 0.8271 (t0) REVERT: B 96 MET cc_start: 0.9223 (ppp) cc_final: 0.9009 (ppp) REVERT: B 110 MET cc_start: 0.7714 (mtp) cc_final: 0.7447 (mmm) REVERT: B 122 HIS cc_start: 0.9301 (m90) cc_final: 0.8645 (m90) REVERT: B 125 VAL cc_start: 0.9565 (t) cc_final: 0.9359 (p) REVERT: B 200 LEU cc_start: 0.9343 (mt) cc_final: 0.8870 (mt) REVERT: B 232 LEU cc_start: 0.8612 (tt) cc_final: 0.8295 (tp) REVERT: B 242 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8988 (t) REVERT: B 302 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.7593 (tpm170) REVERT: B 318 SER cc_start: 0.9799 (t) cc_final: 0.9545 (p) REVERT: B 331 MET cc_start: 0.8478 (tpp) cc_final: 0.7667 (tmm) REVERT: B 383 ASP cc_start: 0.9036 (t0) cc_final: 0.8540 (m-30) REVERT: B 435 MET cc_start: 0.8976 (mmt) cc_final: 0.8046 (mmm) REVERT: B 440 MET cc_start: 0.9308 (tpp) cc_final: 0.9021 (tmm) REVERT: B 442 MET cc_start: 0.9004 (tpp) cc_final: 0.8749 (mmm) REVERT: B 515 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7511 (mm-30) REVERT: B 554 MET cc_start: 0.8411 (tpt) cc_final: 0.8165 (tpt) REVERT: B 577 MET cc_start: 0.8595 (tpp) cc_final: 0.8247 (tpp) REVERT: B 635 ASP cc_start: 0.8562 (t0) cc_final: 0.8225 (t0) REVERT: C 44 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9314 (mp) REVERT: C 96 MET cc_start: 0.9234 (ppp) cc_final: 0.9029 (ppp) REVERT: C 122 HIS cc_start: 0.9271 (m90) cc_final: 0.8599 (m90) REVERT: C 176 GLU cc_start: 0.9426 (pm20) cc_final: 0.9086 (mp0) REVERT: C 177 GLU cc_start: 0.9224 (pm20) cc_final: 0.8909 (pm20) REVERT: C 178 ILE cc_start: 0.9532 (mp) cc_final: 0.9182 (mp) REVERT: C 215 MET cc_start: 0.8792 (mmt) cc_final: 0.8443 (mmp) REVERT: C 302 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7655 (tpp-160) REVERT: C 318 SER cc_start: 0.9779 (t) cc_final: 0.9510 (p) REVERT: C 383 ASP cc_start: 0.9003 (t0) cc_final: 0.8622 (m-30) REVERT: C 435 MET cc_start: 0.9008 (mmt) cc_final: 0.8071 (mmm) REVERT: C 442 MET cc_start: 0.9044 (tpp) cc_final: 0.8753 (mmm) REVERT: C 515 GLU cc_start: 0.7464 (tp30) cc_final: 0.7234 (mm-30) REVERT: C 528 MET cc_start: 0.8671 (tpp) cc_final: 0.8275 (tpp) REVERT: C 577 MET cc_start: 0.8674 (tpp) cc_final: 0.8215 (tpp) REVERT: C 635 ASP cc_start: 0.8496 (t0) cc_final: 0.8174 (t0) REVERT: D 66 LYS cc_start: 0.9496 (tppt) cc_final: 0.9050 (tptp) REVERT: D 96 MET cc_start: 0.9399 (ptt) cc_final: 0.8936 (ptp) REVERT: D 99 MET cc_start: 0.8901 (mpp) cc_final: 0.8639 (ptp) REVERT: D 100 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8425 (mm-30) REVERT: D 110 MET cc_start: 0.7442 (mtp) cc_final: 0.6807 (mmt) REVERT: D 178 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.8756 (mm) REVERT: D 290 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7887 (mm-40) REVERT: D 302 ARG cc_start: 0.8220 (tpm170) cc_final: 0.7715 (tpm170) REVERT: D 318 SER cc_start: 0.9778 (t) cc_final: 0.9506 (p) REVERT: D 331 MET cc_start: 0.8525 (tpp) cc_final: 0.7784 (tmm) REVERT: D 383 ASP cc_start: 0.8899 (t0) cc_final: 0.8374 (m-30) REVERT: D 435 MET cc_start: 0.8868 (mmt) cc_final: 0.7915 (mmt) REVERT: D 440 MET cc_start: 0.9214 (tpt) cc_final: 0.8989 (tmm) REVERT: D 445 ILE cc_start: 0.9599 (tp) cc_final: 0.9355 (pt) REVERT: D 466 MET cc_start: 0.9302 (mtt) cc_final: 0.9036 (mmm) REVERT: D 528 MET cc_start: 0.8761 (tpp) cc_final: 0.8425 (tpp) REVERT: D 554 MET cc_start: 0.8372 (tpt) cc_final: 0.8143 (tpt) REVERT: D 603 MET cc_start: 0.8796 (ttt) cc_final: 0.8442 (tmm) REVERT: D 635 ASP cc_start: 0.8562 (t0) cc_final: 0.8251 (t0) outliers start: 59 outliers final: 38 residues processed: 394 average time/residue: 0.1177 time to fit residues: 76.1694 Evaluate side-chains 394 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 352 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 234 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074528 restraints weight = 54645.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077644 restraints weight = 27015.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079784 restraints weight = 16732.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081246 restraints weight = 11881.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082283 restraints weight = 9298.804| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20209 Z= 0.173 Angle : 0.755 13.691 27424 Z= 0.366 Chirality : 0.043 0.180 3102 Planarity : 0.004 0.050 3454 Dihedral : 8.362 85.116 2805 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.83 % Allowed : 20.14 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.70 (0.17), residues: 2436 helix: 0.04 (0.14), residues: 1376 sheet: -2.85 (0.59), residues: 68 loop : -2.74 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.020 0.001 TYR C 324 PHE 0.011 0.001 PHE A 211 TRP 0.011 0.001 TRP A 629 HIS 0.005 0.001 HIS C 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (20209) covalent geometry : angle 0.75520 / 0.37 (27424) hydrogen bonds : bond 0.03229 / 2.13 ( 760) hydrogen bonds : angle 4.43731 / 3.21 ( 2220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LEU cc_start: 0.9274 (mt) cc_final: 0.8779 (mt) REVERT: A 290 GLN cc_start: 0.8457 (pm20) cc_final: 0.7997 (mm-40) REVERT: A 302 ARG cc_start: 0.8269 (tpm170) cc_final: 0.7839 (tpm170) REVERT: A 331 MET cc_start: 0.8552 (tpp) cc_final: 0.7689 (tmm) REVERT: A 383 ASP cc_start: 0.9073 (t0) cc_final: 0.8609 (m-30) REVERT: A 454 MET cc_start: 0.9050 (tpt) cc_final: 0.8795 (tpt) REVERT: A 466 MET cc_start: 0.9472 (mtt) cc_final: 0.9194 (mmt) REVERT: A 515 GLU cc_start: 0.7511 (tp30) cc_final: 0.7174 (mm-30) REVERT: A 577 MET cc_start: 0.8664 (tpp) cc_final: 0.8425 (tpp) REVERT: A 635 ASP cc_start: 0.8634 (t0) cc_final: 0.8262 (t0) REVERT: B 110 MET cc_start: 0.7712 (mtp) cc_final: 0.7444 (mmm) REVERT: B 122 HIS cc_start: 0.9308 (m90) cc_final: 0.8884 (m-70) REVERT: B 176 GLU cc_start: 0.9381 (pm20) cc_final: 0.9004 (pm20) REVERT: B 242 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9025 (t) REVERT: B 302 ARG cc_start: 0.8012 (tpp-160) cc_final: 0.7738 (tpm170) REVERT: B 318 SER cc_start: 0.9796 (t) cc_final: 0.9536 (p) REVERT: B 331 MET cc_start: 0.8498 (tpp) cc_final: 0.7698 (tmm) REVERT: B 383 ASP cc_start: 0.9099 (t0) cc_final: 0.8606 (m-30) REVERT: B 435 MET cc_start: 0.8876 (mmt) cc_final: 0.7888 (mmm) REVERT: B 440 MET cc_start: 0.9332 (tpp) cc_final: 0.9082 (tmm) REVERT: B 442 MET cc_start: 0.9040 (tpp) cc_final: 0.8769 (mmm) REVERT: B 515 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 554 MET cc_start: 0.8491 (tpt) cc_final: 0.8217 (tpt) REVERT: B 577 MET cc_start: 0.8671 (tpp) cc_final: 0.8397 (tpp) REVERT: B 635 ASP cc_start: 0.8641 (t0) cc_final: 0.8371 (t0) REVERT: C 122 HIS cc_start: 0.9287 (m90) cc_final: 0.8648 (m90) REVERT: C 176 GLU cc_start: 0.9417 (pm20) cc_final: 0.9105 (mp0) REVERT: C 215 MET cc_start: 0.8864 (mmt) cc_final: 0.8538 (mmp) REVERT: C 242 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9053 (t) REVERT: C 302 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7677 (tpp-160) REVERT: C 318 SER cc_start: 0.9786 (t) cc_final: 0.9507 (p) REVERT: C 383 ASP cc_start: 0.9049 (t0) cc_final: 0.8573 (m-30) REVERT: C 435 MET cc_start: 0.8957 (mmt) cc_final: 0.7977 (mmm) REVERT: C 515 GLU cc_start: 0.7608 (tp30) cc_final: 0.7044 (mm-30) REVERT: C 528 MET cc_start: 0.8723 (tpp) cc_final: 0.8342 (tpp) REVERT: C 577 MET cc_start: 0.8649 (tpp) cc_final: 0.8283 (tpp) REVERT: C 635 ASP cc_start: 0.8550 (t0) cc_final: 0.8135 (t0) REVERT: D 66 LYS cc_start: 0.9515 (tppt) cc_final: 0.9069 (tptp) REVERT: D 96 MET cc_start: 0.9444 (ptt) cc_final: 0.8939 (ptp) REVERT: D 99 MET cc_start: 0.8952 (mpp) cc_final: 0.8668 (ptp) REVERT: D 100 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8499 (mm-30) REVERT: D 110 MET cc_start: 0.7451 (mtp) cc_final: 0.6651 (mmt) REVERT: D 178 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9054 (mm) REVERT: D 290 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: D 302 ARG cc_start: 0.8173 (tpm170) cc_final: 0.7685 (tpm170) REVERT: D 318 SER cc_start: 0.9784 (t) cc_final: 0.9515 (p) REVERT: D 331 MET cc_start: 0.8544 (tpp) cc_final: 0.7811 (tmm) REVERT: D 383 ASP cc_start: 0.8914 (t0) cc_final: 0.8394 (m-30) REVERT: D 390 LEU cc_start: 0.9370 (mm) cc_final: 0.9127 (mm) REVERT: D 435 MET cc_start: 0.8855 (mmt) cc_final: 0.7915 (mmt) REVERT: D 440 MET cc_start: 0.9271 (tpt) cc_final: 0.9054 (tmm) REVERT: D 445 ILE cc_start: 0.9602 (tp) cc_final: 0.9375 (pt) REVERT: D 466 MET cc_start: 0.9406 (mtt) cc_final: 0.9009 (mmm) REVERT: D 528 MET cc_start: 0.8789 (tpp) cc_final: 0.8457 (tpp) REVERT: D 554 MET cc_start: 0.8469 (tpt) cc_final: 0.8165 (tpt) REVERT: D 577 MET cc_start: 0.8338 (tpp) cc_final: 0.7969 (tpp) REVERT: D 603 MET cc_start: 0.8783 (ttt) cc_final: 0.8504 (tmm) REVERT: D 635 ASP cc_start: 0.8565 (t0) cc_final: 0.8197 (t0) outliers start: 60 outliers final: 42 residues processed: 390 average time/residue: 0.1126 time to fit residues: 72.3190 Evaluate side-chains 386 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 175 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076564 restraints weight = 53855.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079741 restraints weight = 26359.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081968 restraints weight = 16268.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083474 restraints weight = 11482.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084452 restraints weight = 8958.329| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20209 Z= 0.124 Angle : 0.754 14.231 27424 Z= 0.361 Chirality : 0.043 0.173 3102 Planarity : 0.004 0.051 3454 Dihedral : 8.034 89.360 2805 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.41 % Allowed : 20.71 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.56 (0.18), residues: 2436 helix: 0.21 (0.15), residues: 1352 sheet: -2.79 (0.59), residues: 68 loop : -2.70 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.020 0.001 TYR C 324 PHE 0.012 0.001 PHE B 211 TRP 0.010 0.001 TRP B 629 HIS 0.005 0.001 HIS C 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (20209) covalent geometry : angle 0.75424 / 0.36 (27424) hydrogen bonds : bond 0.03078 / 2.02 ( 760) hydrogen bonds : angle 4.22907 / 3.06 ( 2220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 370 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6762 (t-100) cc_final: 0.6389 (t60) REVERT: A 122 HIS cc_start: 0.9314 (m90) cc_final: 0.8547 (m90) REVERT: A 200 LEU cc_start: 0.9240 (mt) cc_final: 0.8736 (mt) REVERT: A 242 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9025 (t) REVERT: A 290 GLN cc_start: 0.8374 (pm20) cc_final: 0.7934 (mm-40) REVERT: A 302 ARG cc_start: 0.8383 (tpm170) cc_final: 0.7934 (tpm170) REVERT: A 331 MET cc_start: 0.8525 (tpp) cc_final: 0.7621 (tmm) REVERT: A 383 ASP cc_start: 0.9057 (t0) cc_final: 0.8581 (m-30) REVERT: A 435 MET cc_start: 0.8795 (mmt) cc_final: 0.7784 (mmt) REVERT: A 440 MET cc_start: 0.9375 (tpp) cc_final: 0.9147 (tmm) REVERT: A 454 MET cc_start: 0.9002 (tpt) cc_final: 0.8785 (tpt) REVERT: A 466 MET cc_start: 0.9415 (mtt) cc_final: 0.9171 (mmt) REVERT: A 515 GLU cc_start: 0.7393 (tp30) cc_final: 0.6915 (mm-30) REVERT: A 577 MET cc_start: 0.8583 (tpp) cc_final: 0.8274 (tpp) REVERT: A 608 LEU cc_start: 0.9427 (mp) cc_final: 0.9079 (tt) REVERT: A 635 ASP cc_start: 0.8590 (t0) cc_final: 0.8324 (t0) REVERT: B 110 MET cc_start: 0.7742 (mtp) cc_final: 0.7517 (mmm) REVERT: B 113 GLU cc_start: 0.9388 (tt0) cc_final: 0.9051 (tp30) REVERT: B 122 HIS cc_start: 0.9291 (m90) cc_final: 0.8846 (m-70) REVERT: B 125 VAL cc_start: 0.9564 (t) cc_final: 0.9359 (p) REVERT: B 176 GLU cc_start: 0.9365 (pm20) cc_final: 0.9021 (pm20) REVERT: B 242 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9005 (t) REVERT: B 302 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7751 (tpm170) REVERT: B 318 SER cc_start: 0.9796 (t) cc_final: 0.9536 (p) REVERT: B 331 MET cc_start: 0.8512 (tpp) cc_final: 0.7677 (tmm) REVERT: B 383 ASP cc_start: 0.9069 (t0) cc_final: 0.8598 (m-30) REVERT: B 435 MET cc_start: 0.8844 (mmt) cc_final: 0.7816 (mmm) REVERT: B 440 MET cc_start: 0.9337 (tpp) cc_final: 0.9099 (tmm) REVERT: B 442 MET cc_start: 0.9004 (tpp) cc_final: 0.8765 (mmm) REVERT: B 474 MET cc_start: 0.8790 (tpp) cc_final: 0.8538 (tpp) REVERT: B 554 MET cc_start: 0.8411 (tpt) cc_final: 0.8159 (tpt) REVERT: B 577 MET cc_start: 0.8653 (tpp) cc_final: 0.8369 (tpp) REVERT: B 608 LEU cc_start: 0.9405 (mp) cc_final: 0.9076 (tt) REVERT: B 635 ASP cc_start: 0.8599 (t0) cc_final: 0.8317 (t0) REVERT: C 122 HIS cc_start: 0.9255 (m90) cc_final: 0.8531 (m90) REVERT: C 173 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8270 (p) REVERT: C 176 GLU cc_start: 0.9418 (pm20) cc_final: 0.9082 (mp0) REVERT: C 177 GLU cc_start: 0.9245 (pm20) cc_final: 0.8778 (pm20) REVERT: C 242 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9034 (t) REVERT: C 290 GLN cc_start: 0.8490 (pm20) cc_final: 0.7754 (mm-40) REVERT: C 302 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7717 (tpp-160) REVERT: C 318 SER cc_start: 0.9785 (t) cc_final: 0.9517 (p) REVERT: C 383 ASP cc_start: 0.9045 (t0) cc_final: 0.8517 (m-30) REVERT: C 435 MET cc_start: 0.8968 (mmt) cc_final: 0.7978 (mmm) REVERT: C 515 GLU cc_start: 0.7435 (tp30) cc_final: 0.7207 (mm-30) REVERT: C 528 MET cc_start: 0.8665 (tpp) cc_final: 0.8287 (tpp) REVERT: C 577 MET cc_start: 0.8675 (tpp) cc_final: 0.8031 (tpp) REVERT: C 635 ASP cc_start: 0.8521 (t0) cc_final: 0.8105 (t0) REVERT: D 29 TRP cc_start: 0.6802 (t-100) cc_final: 0.6460 (t60) REVERT: D 66 LYS cc_start: 0.9498 (tppt) cc_final: 0.9022 (tptp) REVERT: D 96 MET cc_start: 0.9433 (ptt) cc_final: 0.8907 (ptp) REVERT: D 99 MET cc_start: 0.8962 (mpp) cc_final: 0.8674 (ptp) REVERT: D 100 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8525 (mm-30) REVERT: D 177 GLU cc_start: 0.9025 (pm20) cc_final: 0.8757 (pm20) REVERT: D 178 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8883 (mm) REVERT: D 260 MET cc_start: 0.8893 (mmm) cc_final: 0.8665 (tpp) REVERT: D 290 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7883 (mm-40) REVERT: D 302 ARG cc_start: 0.8206 (tpm170) cc_final: 0.7770 (tpm170) REVERT: D 318 SER cc_start: 0.9777 (t) cc_final: 0.9498 (p) REVERT: D 331 MET cc_start: 0.8514 (tpp) cc_final: 0.7778 (tmm) REVERT: D 383 ASP cc_start: 0.8884 (t0) cc_final: 0.8385 (m-30) REVERT: D 435 MET cc_start: 0.8831 (mmt) cc_final: 0.7857 (mmt) REVERT: D 440 MET cc_start: 0.9238 (tpt) cc_final: 0.9026 (tmm) REVERT: D 466 MET cc_start: 0.9410 (mtt) cc_final: 0.8998 (mmm) REVERT: D 528 MET cc_start: 0.8705 (tpp) cc_final: 0.8352 (tpp) REVERT: D 554 MET cc_start: 0.8372 (tpt) cc_final: 0.8094 (tpt) REVERT: D 603 MET cc_start: 0.8782 (ttt) cc_final: 0.8518 (tmm) REVERT: D 635 ASP cc_start: 0.8553 (t0) cc_final: 0.8273 (t0) outliers start: 51 outliers final: 32 residues processed: 400 average time/residue: 0.1196 time to fit residues: 79.0805 Evaluate side-chains 392 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 354 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076123 restraints weight = 53553.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079303 restraints weight = 26358.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081484 restraints weight = 16268.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082983 restraints weight = 11570.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083991 restraints weight = 9046.836| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20209 Z= 0.129 Angle : 0.783 13.531 27424 Z= 0.372 Chirality : 0.044 0.206 3102 Planarity : 0.004 0.048 3454 Dihedral : 7.764 89.424 2805 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.31 % Allowed : 21.04 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.56 (0.17), residues: 2436 helix: 0.18 (0.15), residues: 1356 sheet: -2.82 (0.59), residues: 68 loop : -2.66 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 385 TYR 0.020 0.001 TYR C 324 PHE 0.011 0.001 PHE C 211 TRP 0.009 0.001 TRP A 629 HIS 0.005 0.001 HIS C 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (20209) covalent geometry : angle 0.78257 / 0.37 (27424) hydrogen bonds : bond 0.03077 / 2.00 ( 760) hydrogen bonds : angle 4.32140 / 3.11 ( 2220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 368 time to evaluate : 0.774 Fit side-chains REVERT: A 29 TRP cc_start: 0.6767 (t-100) cc_final: 0.6401 (t60) REVERT: A 113 GLU cc_start: 0.9380 (tt0) cc_final: 0.9048 (tp30) REVERT: A 200 LEU cc_start: 0.9241 (mt) cc_final: 0.8710 (mt) REVERT: A 232 LEU cc_start: 0.8643 (tt) cc_final: 0.8287 (tp) REVERT: A 242 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9002 (t) REVERT: A 290 GLN cc_start: 0.8406 (pm20) cc_final: 0.7996 (mm-40) REVERT: A 302 ARG cc_start: 0.8386 (tpm170) cc_final: 0.7932 (tpm170) REVERT: A 331 MET cc_start: 0.8522 (tpp) cc_final: 0.7627 (tmm) REVERT: A 383 ASP cc_start: 0.9040 (t0) cc_final: 0.8562 (m-30) REVERT: A 435 MET cc_start: 0.8792 (mmt) cc_final: 0.7769 (mmt) REVERT: A 440 MET cc_start: 0.9388 (tpp) cc_final: 0.9091 (tmm) REVERT: A 466 MET cc_start: 0.9408 (mtt) cc_final: 0.9142 (mmt) REVERT: A 515 GLU cc_start: 0.7374 (tp30) cc_final: 0.6914 (mm-30) REVERT: A 577 MET cc_start: 0.8574 (tpp) cc_final: 0.8269 (tpp) REVERT: A 608 LEU cc_start: 0.9410 (mp) cc_final: 0.9074 (tt) REVERT: A 635 ASP cc_start: 0.8600 (t0) cc_final: 0.8331 (t0) REVERT: B 99 MET cc_start: 0.8844 (ptp) cc_final: 0.8626 (ptp) REVERT: B 110 MET cc_start: 0.7756 (mtp) cc_final: 0.7541 (mmm) REVERT: B 113 GLU cc_start: 0.9376 (tt0) cc_final: 0.9052 (tp30) REVERT: B 125 VAL cc_start: 0.9562 (t) cc_final: 0.9357 (p) REVERT: B 176 GLU cc_start: 0.9374 (pm20) cc_final: 0.9051 (pm20) REVERT: B 242 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8990 (t) REVERT: B 302 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7686 (tpm170) REVERT: B 318 SER cc_start: 0.9793 (t) cc_final: 0.9525 (p) REVERT: B 331 MET cc_start: 0.8472 (tpp) cc_final: 0.7667 (tmm) REVERT: B 383 ASP cc_start: 0.9055 (t0) cc_final: 0.8581 (m-30) REVERT: B 435 MET cc_start: 0.8877 (mmt) cc_final: 0.7914 (mmm) REVERT: B 440 MET cc_start: 0.9371 (tpp) cc_final: 0.9140 (tmm) REVERT: B 442 MET cc_start: 0.9019 (tpp) cc_final: 0.8760 (mmm) REVERT: B 474 MET cc_start: 0.8893 (tpp) cc_final: 0.8650 (tpp) REVERT: B 554 MET cc_start: 0.8399 (tpt) cc_final: 0.8154 (tpt) REVERT: B 577 MET cc_start: 0.8602 (tpp) cc_final: 0.8277 (tpp) REVERT: B 608 LEU cc_start: 0.9391 (mp) cc_final: 0.9072 (tt) REVERT: B 635 ASP cc_start: 0.8590 (t0) cc_final: 0.8310 (t0) REVERT: C 113 GLU cc_start: 0.9373 (tt0) cc_final: 0.9071 (tp30) REVERT: C 122 HIS cc_start: 0.9244 (m90) cc_final: 0.8796 (m-70) REVERT: C 173 VAL cc_start: 0.8429 (t) cc_final: 0.8189 (p) REVERT: C 177 GLU cc_start: 0.9218 (pm20) cc_final: 0.8979 (pm20) REVERT: C 242 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9032 (t) REVERT: C 290 GLN cc_start: 0.8505 (pm20) cc_final: 0.7774 (mm-40) REVERT: C 302 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7738 (tpp-160) REVERT: C 318 SER cc_start: 0.9786 (t) cc_final: 0.9517 (p) REVERT: C 383 ASP cc_start: 0.8987 (t0) cc_final: 0.8603 (m-30) REVERT: C 435 MET cc_start: 0.8983 (mmt) cc_final: 0.8032 (mmm) REVERT: C 515 GLU cc_start: 0.7422 (tp30) cc_final: 0.6958 (mm-30) REVERT: C 528 MET cc_start: 0.8681 (tpp) cc_final: 0.8274 (tpp) REVERT: C 608 LEU cc_start: 0.9383 (mp) cc_final: 0.9055 (tt) REVERT: C 635 ASP cc_start: 0.8515 (t0) cc_final: 0.8102 (t0) REVERT: D 29 TRP cc_start: 0.6837 (t-100) cc_final: 0.6489 (t60) REVERT: D 66 LYS cc_start: 0.9497 (tppt) cc_final: 0.9025 (tptp) REVERT: D 110 MET cc_start: 0.7424 (mtp) cc_final: 0.6858 (mmt) REVERT: D 178 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8976 (mm) REVERT: D 290 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7871 (mm-40) REVERT: D 302 ARG cc_start: 0.8220 (tpm170) cc_final: 0.7770 (tpm170) REVERT: D 318 SER cc_start: 0.9765 (t) cc_final: 0.9509 (p) REVERT: D 331 MET cc_start: 0.8503 (tpp) cc_final: 0.7770 (tmm) REVERT: D 383 ASP cc_start: 0.9000 (t0) cc_final: 0.8591 (m-30) REVERT: D 435 MET cc_start: 0.8832 (mmt) cc_final: 0.7893 (mmt) REVERT: D 466 MET cc_start: 0.9405 (mtt) cc_final: 0.8960 (mmm) REVERT: D 528 MET cc_start: 0.8744 (tpp) cc_final: 0.8395 (tpp) REVERT: D 554 MET cc_start: 0.8381 (tpt) cc_final: 0.8116 (tpt) REVERT: D 603 MET cc_start: 0.8820 (ttt) cc_final: 0.8534 (tmm) REVERT: D 635 ASP cc_start: 0.8563 (t0) cc_final: 0.8279 (t0) outliers start: 49 outliers final: 35 residues processed: 396 average time/residue: 0.1199 time to fit residues: 78.4430 Evaluate side-chains 398 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 0.0970 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 0.0270 chunk 158 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 194 optimal weight: 0.4980 chunk 214 optimal weight: 4.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 206 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.101028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079146 restraints weight = 53264.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082396 restraints weight = 26154.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084619 restraints weight = 16089.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086178 restraints weight = 11392.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087184 restraints weight = 8878.901| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20209 Z= 0.125 Angle : 0.812 15.651 27424 Z= 0.381 Chirality : 0.044 0.251 3102 Planarity : 0.004 0.052 3454 Dihedral : 7.158 81.023 2805 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.37 % Allowed : 22.17 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.63 (0.17), residues: 2436 helix: 0.09 (0.15), residues: 1356 sheet: -2.73 (0.59), residues: 68 loop : -2.65 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.021 0.001 TYR C 324 PHE 0.012 0.001 PHE B 211 TRP 0.007 0.001 TRP A 629 HIS 0.004 0.000 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (20209) covalent geometry : angle 0.81174 / 0.38 (27424) hydrogen bonds : bond 0.03089 / 2.00 ( 760) hydrogen bonds : angle 4.21561 / 3.04 ( 2220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 373 time to evaluate : 0.796 Fit side-chains REVERT: A 29 TRP cc_start: 0.6775 (t-100) cc_final: 0.6443 (t60) REVERT: A 99 MET cc_start: 0.8587 (ptp) cc_final: 0.8289 (ptt) REVERT: A 113 GLU cc_start: 0.9348 (tt0) cc_final: 0.9033 (tp30) REVERT: A 200 LEU cc_start: 0.9181 (mt) cc_final: 0.8673 (mt) REVERT: A 232 LEU cc_start: 0.8612 (tt) cc_final: 0.8240 (tp) REVERT: A 242 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8946 (t) REVERT: A 290 GLN cc_start: 0.8334 (pm20) cc_final: 0.7906 (mm-40) REVERT: A 302 ARG cc_start: 0.8438 (tpm170) cc_final: 0.8031 (tpm170) REVERT: A 331 MET cc_start: 0.8461 (tpp) cc_final: 0.7550 (tmm) REVERT: A 383 ASP cc_start: 0.9057 (t0) cc_final: 0.8591 (m-30) REVERT: A 435 MET cc_start: 0.8759 (mmt) cc_final: 0.7739 (mmt) REVERT: A 440 MET cc_start: 0.9353 (tpp) cc_final: 0.9100 (tmm) REVERT: A 466 MET cc_start: 0.9374 (mtt) cc_final: 0.9085 (mmm) REVERT: A 515 GLU cc_start: 0.7278 (tp30) cc_final: 0.6880 (mm-30) REVERT: A 568 LEU cc_start: 0.8895 (mp) cc_final: 0.8678 (mp) REVERT: A 577 MET cc_start: 0.8480 (tpp) cc_final: 0.8243 (tpp) REVERT: A 608 LEU cc_start: 0.9320 (mp) cc_final: 0.8958 (tt) REVERT: A 635 ASP cc_start: 0.8599 (t0) cc_final: 0.8313 (t0) REVERT: B 29 TRP cc_start: 0.6846 (t-100) cc_final: 0.6475 (t60) REVERT: B 110 MET cc_start: 0.7766 (mtp) cc_final: 0.7547 (mmm) REVERT: B 113 GLU cc_start: 0.9326 (tt0) cc_final: 0.9025 (tp30) REVERT: B 122 HIS cc_start: 0.9270 (m90) cc_final: 0.8825 (m-70) REVERT: B 125 VAL cc_start: 0.9531 (t) cc_final: 0.9322 (p) REVERT: B 242 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8912 (t) REVERT: B 302 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7822 (tpm170) REVERT: B 318 SER cc_start: 0.9788 (t) cc_final: 0.9521 (p) REVERT: B 331 MET cc_start: 0.8456 (tpp) cc_final: 0.7624 (tmm) REVERT: B 383 ASP cc_start: 0.9068 (t0) cc_final: 0.8598 (m-30) REVERT: B 435 MET cc_start: 0.8825 (mmt) cc_final: 0.7845 (mmm) REVERT: B 440 MET cc_start: 0.9307 (tpp) cc_final: 0.9084 (tmm) REVERT: B 464 ASN cc_start: 0.8888 (t0) cc_final: 0.8423 (t0) REVERT: B 515 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 554 MET cc_start: 0.8335 (tpt) cc_final: 0.8114 (tpt) REVERT: B 568 LEU cc_start: 0.9233 (tp) cc_final: 0.8787 (tp) REVERT: B 577 MET cc_start: 0.8450 (tpp) cc_final: 0.8103 (tpp) REVERT: B 608 LEU cc_start: 0.9324 (mp) cc_final: 0.8979 (tt) REVERT: B 635 ASP cc_start: 0.8584 (t0) cc_final: 0.8306 (t0) REVERT: C 29 TRP cc_start: 0.6743 (t-100) cc_final: 0.6454 (t60) REVERT: C 99 MET cc_start: 0.9040 (ptp) cc_final: 0.8611 (ptt) REVERT: C 113 GLU cc_start: 0.9325 (tt0) cc_final: 0.9088 (tp30) REVERT: C 122 HIS cc_start: 0.9261 (m90) cc_final: 0.8523 (m90) REVERT: C 176 GLU cc_start: 0.9326 (pm20) cc_final: 0.8877 (pm20) REVERT: C 215 MET cc_start: 0.8892 (mmt) cc_final: 0.8622 (mmp) REVERT: C 242 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8976 (t) REVERT: C 302 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7663 (tpm170) REVERT: C 318 SER cc_start: 0.9775 (t) cc_final: 0.9506 (p) REVERT: C 383 ASP cc_start: 0.9051 (t0) cc_final: 0.8533 (m-30) REVERT: C 435 MET cc_start: 0.8955 (mmt) cc_final: 0.7993 (mmm) REVERT: C 464 ASN cc_start: 0.8888 (t0) cc_final: 0.8424 (t0) REVERT: C 515 GLU cc_start: 0.7357 (tp30) cc_final: 0.6987 (mm-30) REVERT: C 528 MET cc_start: 0.8537 (tpp) cc_final: 0.8071 (tpp) REVERT: C 587 HIS cc_start: 0.8595 (p-80) cc_final: 0.8146 (t70) REVERT: C 608 LEU cc_start: 0.9343 (mp) cc_final: 0.8974 (tt) REVERT: C 635 ASP cc_start: 0.8484 (t0) cc_final: 0.8180 (t0) REVERT: D 29 TRP cc_start: 0.6721 (t-100) cc_final: 0.6409 (t60) REVERT: D 66 LYS cc_start: 0.9491 (tppt) cc_final: 0.9026 (tptp) REVERT: D 96 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.8887 (ptp) REVERT: D 99 MET cc_start: 0.9081 (ptp) cc_final: 0.8304 (ptp) REVERT: D 110 MET cc_start: 0.7345 (mtp) cc_final: 0.6735 (mmt) REVERT: D 178 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9090 (mm) REVERT: D 260 MET cc_start: 0.8841 (mmm) cc_final: 0.8421 (tpp) REVERT: D 280 LEU cc_start: 0.8438 (tp) cc_final: 0.8155 (tp) REVERT: D 290 GLN cc_start: 0.8610 (pm20) cc_final: 0.7727 (mm-40) REVERT: D 302 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7793 (tpm170) REVERT: D 315 GLU cc_start: 0.9131 (tp30) cc_final: 0.8686 (tp30) REVERT: D 318 SER cc_start: 0.9751 (t) cc_final: 0.9479 (p) REVERT: D 331 MET cc_start: 0.8466 (tpp) cc_final: 0.7742 (tmm) REVERT: D 383 ASP cc_start: 0.9092 (t0) cc_final: 0.8684 (m-30) REVERT: D 435 MET cc_start: 0.8788 (mmt) cc_final: 0.7828 (mmt) REVERT: D 464 ASN cc_start: 0.8876 (t0) cc_final: 0.8372 (t0) REVERT: D 466 MET cc_start: 0.9385 (mtt) cc_final: 0.8935 (mmm) REVERT: D 528 MET cc_start: 0.8702 (tpp) cc_final: 0.8345 (tpp) REVERT: D 554 MET cc_start: 0.8280 (tpt) cc_final: 0.8065 (tpt) REVERT: D 587 HIS cc_start: 0.8648 (p-80) cc_final: 0.8253 (t70) REVERT: D 603 MET cc_start: 0.8811 (ttt) cc_final: 0.8534 (tmm) REVERT: D 608 LEU cc_start: 0.9383 (mp) cc_final: 0.9079 (tt) REVERT: D 635 ASP cc_start: 0.8572 (t0) cc_final: 0.8238 (t0) outliers start: 29 outliers final: 20 residues processed: 387 average time/residue: 0.1177 time to fit residues: 75.7822 Evaluate side-chains 384 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 359 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077814 restraints weight = 53871.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081068 restraints weight = 26450.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083314 restraints weight = 16262.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084854 restraints weight = 11492.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085848 restraints weight = 8972.089| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20209 Z= 0.129 Angle : 0.810 13.052 27424 Z= 0.383 Chirality : 0.044 0.212 3102 Planarity : 0.004 0.048 3454 Dihedral : 6.939 80.262 2805 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.23 % Allowed : 22.74 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.57 (0.17), residues: 2436 helix: 0.12 (0.15), residues: 1356 sheet: -2.65 (0.60), residues: 68 loop : -2.59 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.021 0.001 TYR C 324 PHE 0.011 0.001 PHE B 211 TRP 0.008 0.001 TRP B 629 HIS 0.004 0.000 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (20209) covalent geometry : angle 0.80951 / 0.38 (27424) hydrogen bonds : bond 0.02990 / 1.94 ( 760) hydrogen bonds : angle 4.26658 / 3.06 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.81 seconds wall clock time: 69 minutes 44.97 seconds (4184.97 seconds total)