Starting phenix.real_space_refine on Sun Aug 24 12:48:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4c_22664/08_2025/7k4c_22664_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4c_22664/08_2025/7k4c_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k4c_22664/08_2025/7k4c_22664_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4c_22664/08_2025/7k4c_22664_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k4c_22664/08_2025/7k4c_22664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4c_22664/08_2025/7k4c_22664.map" } 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-2.0-5787/lib/python3.9/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, 28 Unusual residues: {' CA': 2, '81F': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 5.10, per 1000 atoms: 0.26 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: 1.55 Conformation dependent library (CDL) restraints added in 951.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.62 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: 3.57 Time building geometry restraints manager: 2.06 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.450 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 aren 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 covalent geometry : bond 0.00926 (20209) covalent geometry : angle 1.08836 (27424) hydrogen bonds : bond 0.30745 ( 760) hydrogen bonds : angle 8.92258 ( 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 : 0.690 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: 0.7414 (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: 0.8733 (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: 0.7266 (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: 0.8780 (tt0) REVERT: A 590 ASP cc_start: 0.8562 (m-30) cc_final: 0.8077 (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: 0.8705 (m-30) REVERT: B 386 LEU cc_start: 0.9376 (tp) cc_final: 0.9138 (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: 0.8596 (p-80) REVERT: B 588 GLU cc_start: 0.9060 (tt0) cc_final: 0.8753 (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: 0.1485 time to fit residues: 133.6803 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 : 1.047 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.099514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077769 restraints weight = 55516.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080916 restraints weight = 26819.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083095 restraints weight = 16479.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084576 restraints weight = 11639.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085550 restraints weight = 9107.979| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20209 Z= 0.148 Angle : 0.752 10.395 27424 Z= 0.381 Chirality : 0.042 0.153 3102 Planarity : 0.005 0.071 3454 Dihedral : 9.565 89.640 2805 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.89 % Allowed : 13.58 % Favored : 84.53 % 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 aren not related in a simple way. whole: -3.62 (0.15), residues: 2436 helix: -1.79 (0.12), residues: 1388 sheet: -3.04 (0.54), residues: 68 loop : -3.18 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 302 TYR 0.034 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 covalent geometry : bond 0.00317 (20209) covalent geometry : angle 0.75172 (27424) hydrogen bonds : bond 0.05099 ( 760) hydrogen bonds : angle 5.31441 ( 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 479 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 439 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9436 (pp) cc_final: 0.9036 (pt) REVERT: A 96 MET cc_start: 0.9098 (mmm) cc_final: 0.8534 (mmp) REVERT: A 122 HIS cc_start: 0.9452 (m90) cc_final: 0.8723 (m90) REVERT: A 345 MET cc_start: 0.8698 (tpp) cc_final: 0.8354 (tpp) REVERT: A 383 ASP cc_start: 0.9106 (t0) cc_final: 0.8631 (m-30) REVERT: A 435 MET cc_start: 0.8860 (mmt) cc_final: 0.8054 (mmm) REVERT: A 444 LEU cc_start: 0.9572 (mp) cc_final: 0.9209 (mt) REVERT: A 466 MET cc_start: 0.9444 (mtt) cc_final: 0.9154 (mmt) REVERT: A 515 GLU cc_start: 0.7576 (tp30) cc_final: 0.7124 (mm-30) REVERT: A 554 MET cc_start: 0.8467 (tpt) cc_final: 0.8226 (tpt) REVERT: A 587 HIS cc_start: 0.8914 (p-80) cc_final: 0.8237 (p-80) REVERT: A 588 GLU cc_start: 0.9018 (tt0) cc_final: 0.8814 (tt0) REVERT: A 590 ASP cc_start: 0.8654 (m-30) cc_final: 0.8111 (p0) REVERT: A 635 ASP cc_start: 0.8661 (t0) cc_final: 0.8296 (t0) REVERT: B 92 LEU cc_start: 0.9443 (pp) cc_final: 0.9069 (pt) REVERT: B 122 HIS cc_start: 0.9467 (m90) cc_final: 0.8765 (m90) REVERT: B 132 LEU cc_start: 0.9155 (mt) cc_final: 0.8934 (mt) REVERT: B 159 LEU cc_start: 0.9420 (tp) cc_final: 0.9115 (tt) REVERT: B 267 GLN cc_start: 0.8371 (tt0) cc_final: 0.8157 (tp-100) REVERT: B 318 SER cc_start: 0.9785 (t) cc_final: 0.9547 (p) REVERT: B 383 ASP cc_start: 0.9100 (t0) cc_final: 0.8612 (m-30) REVERT: B 435 MET cc_start: 0.8898 (mmt) cc_final: 0.8095 (mmm) REVERT: B 442 MET cc_start: 0.9071 (tpp) cc_final: 0.8827 (mmm) REVERT: B 444 LEU cc_start: 0.9553 (mp) cc_final: 0.9198 (mt) REVERT: B 485 MET cc_start: 0.8237 (ttm) cc_final: 0.7459 (ttm) REVERT: B 554 MET cc_start: 0.8622 (tpt) cc_final: 0.8343 (tpt) REVERT: B 577 MET cc_start: 0.8735 (tpp) cc_final: 0.8374 (tpp) REVERT: B 587 HIS cc_start: 0.8930 (p-80) cc_final: 0.8280 (p-80) REVERT: B 590 ASP cc_start: 0.8711 (m-30) cc_final: 0.8087 (p0) REVERT: C 92 LEU cc_start: 0.9466 (pp) cc_final: 0.9083 (pt) REVERT: C 122 HIS cc_start: 0.9444 (m90) cc_final: 0.8719 (m90) REVERT: C 159 LEU cc_start: 0.9444 (tp) cc_final: 0.9134 (tt) REVERT: C 318 SER cc_start: 0.9769 (t) cc_final: 0.9517 (p) REVERT: C 383 ASP cc_start: 0.9107 (t0) cc_final: 0.8646 (m-30) REVERT: C 435 MET cc_start: 0.8935 (mmt) cc_final: 0.8073 (mmt) REVERT: C 442 MET cc_start: 0.9137 (tpp) cc_final: 0.8548 (tpp) REVERT: C 515 GLU cc_start: 0.7607 (tp30) cc_final: 0.7337 (mm-30) REVERT: C 528 MET cc_start: 0.8607 (tpp) cc_final: 0.8323 (tpp) REVERT: C 587 HIS cc_start: 0.8919 (p-80) cc_final: 0.8270 (p-80) REVERT: C 588 GLU cc_start: 0.8974 (tt0) cc_final: 0.8765 (tt0) REVERT: C 590 ASP cc_start: 0.8703 (m-30) cc_final: 0.8064 (p0) REVERT: D 29 TRP cc_start: 0.6823 (t-100) cc_final: 0.6397 (t60) REVERT: D 66 LYS cc_start: 0.9497 (tppt) cc_final: 0.9024 (tptp) REVERT: D 92 LEU cc_start: 0.9500 (pp) cc_final: 0.9087 (pt) REVERT: D 96 MET cc_start: 0.9030 (mmm) cc_final: 0.8399 (mmp) REVERT: D 122 HIS cc_start: 0.9523 (m90) cc_final: 0.8917 (m90) REVERT: D 137 LEU cc_start: 0.9738 (mp) cc_final: 0.9496 (pp) REVERT: D 178 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.8920 (mm) REVERT: D 315 GLU cc_start: 0.9199 (tp30) cc_final: 0.8695 (tp30) REVERT: D 318 SER cc_start: 0.9742 (t) cc_final: 0.9450 (p) REVERT: D 383 ASP cc_start: 0.9065 (t0) cc_final: 0.8493 (m-30) REVERT: D 435 MET cc_start: 0.8832 (mmt) cc_final: 0.8033 (mmt) REVERT: D 440 MET cc_start: 0.9092 (tpt) cc_final: 0.8881 (tpp) REVERT: D 444 LEU cc_start: 0.9566 (mp) cc_final: 0.9230 (mt) REVERT: D 466 MET cc_start: 0.9424 (mtt) cc_final: 0.8990 (mmt) REVERT: D 485 MET cc_start: 0.8135 (ttm) cc_final: 0.7783 (ttm) REVERT: D 554 MET cc_start: 0.8601 (tpt) cc_final: 0.8316 (tpt) REVERT: D 578 MET cc_start: 0.8142 (mmt) cc_final: 0.7878 (mmt) REVERT: D 587 HIS cc_start: 0.8907 (p-80) cc_final: 0.8556 (p-80) REVERT: D 588 GLU cc_start: 0.8880 (tt0) cc_final: 0.8344 (tm-30) REVERT: D 590 ASP cc_start: 0.8700 (m-30) cc_final: 0.8252 (p0) REVERT: D 603 MET cc_start: 0.8785 (ttt) cc_final: 0.8503 (tmm) outliers start: 40 outliers final: 20 residues processed: 460 average time/residue: 0.1285 time to fit residues: 93.8909 Evaluate side-chains 388 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 367 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 118 GLN 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 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: 4.9990 chunk 77 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 258 HIS B 464 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078033 restraints weight = 55181.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.081229 restraints weight = 26698.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083421 restraints weight = 16460.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084924 restraints weight = 11689.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085998 restraints weight = 9171.521| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20209 Z= 0.124 Angle : 0.691 11.324 27424 Z= 0.343 Chirality : 0.041 0.151 3102 Planarity : 0.004 0.068 3454 Dihedral : 9.422 89.826 2805 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.69 % Allowed : 14.62 % Favored : 82.69 % 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 aren not related in a simple way. whole: -2.77 (0.16), residues: 2436 helix: -0.90 (0.13), residues: 1336 sheet: -3.02 (0.55), residues: 68 loop : -3.04 (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 0.018 0.001 PHE D 162 TRP 0.009 0.001 TRP A 583 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00276 (20209) covalent geometry : angle 0.69056 (27424) hydrogen bonds : bond 0.03995 ( 760) hydrogen bonds : angle 4.77535 ( 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 453 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 396 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9460 (pp) cc_final: 0.8986 (pt) REVERT: A 122 HIS cc_start: 0.9364 (m90) cc_final: 0.8639 (m90) REVERT: A 132 LEU cc_start: 0.9176 (mt) cc_final: 0.8974 (mt) REVERT: A 177 GLU cc_start: 0.9502 (pm20) cc_final: 0.9223 (pm20) REVERT: A 290 GLN cc_start: 0.8326 (pp30) cc_final: 0.7842 (pp30) REVERT: A 302 ARG cc_start: 0.8205 (tpm170) cc_final: 0.7467 (tpm170) REVERT: A 383 ASP cc_start: 0.9024 (t0) cc_final: 0.8601 (m-30) REVERT: A 444 LEU cc_start: 0.9495 (mp) cc_final: 0.9265 (mt) REVERT: A 466 MET cc_start: 0.9366 (mtt) cc_final: 0.9156 (mmt) REVERT: A 474 MET cc_start: 0.8721 (tpp) cc_final: 0.8504 (tpp) REVERT: A 485 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7871 (tpp) REVERT: A 515 GLU cc_start: 0.7333 (tp30) cc_final: 0.6834 (mm-30) REVERT: A 528 MET cc_start: 0.8347 (tpp) cc_final: 0.8083 (tpp) REVERT: A 578 MET cc_start: 0.8263 (mmt) cc_final: 0.7819 (mmt) REVERT: A 587 HIS cc_start: 0.8791 (p-80) cc_final: 0.8288 (p-80) REVERT: A 590 ASP cc_start: 0.8571 (m-30) cc_final: 0.7993 (p0) REVERT: A 635 ASP cc_start: 0.8595 (t0) cc_final: 0.8182 (t0) REVERT: B 92 LEU cc_start: 0.9447 (pp) cc_final: 0.9036 (pp) REVERT: B 122 HIS cc_start: 0.9356 (m90) cc_final: 0.8655 (m90) REVERT: B 159 LEU cc_start: 0.9426 (tp) cc_final: 0.9127 (tt) REVERT: B 200 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9001 (mt) REVERT: B 302 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7607 (tpp-160) REVERT: B 318 SER cc_start: 0.9783 (t) cc_final: 0.9546 (p) REVERT: B 383 ASP cc_start: 0.9023 (t0) cc_final: 0.8546 (m-30) REVERT: B 440 MET cc_start: 0.9266 (tpp) cc_final: 0.9056 (tpp) REVERT: B 442 MET cc_start: 0.9095 (tpp) cc_final: 0.8852 (mmm) REVERT: B 444 LEU cc_start: 0.9488 (mp) cc_final: 0.9245 (mt) REVERT: B 485 MET cc_start: 0.8102 (ttm) cc_final: 0.7536 (ttm) REVERT: B 515 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 528 MET cc_start: 0.8512 (tpp) cc_final: 0.8272 (tpp) REVERT: B 554 MET cc_start: 0.8493 (tpt) cc_final: 0.8193 (tpt) REVERT: B 577 MET cc_start: 0.8636 (tpp) cc_final: 0.8360 (tpp) REVERT: B 578 MET cc_start: 0.8129 (mmt) cc_final: 0.7764 (mmt) REVERT: B 587 HIS cc_start: 0.8811 (p-80) cc_final: 0.8296 (p-80) REVERT: B 590 ASP cc_start: 0.8694 (m-30) cc_final: 0.8031 (p0) REVERT: C 122 HIS cc_start: 0.9388 (m90) cc_final: 0.8707 (m90) REVERT: C 318 SER cc_start: 0.9768 (t) cc_final: 0.9518 (p) REVERT: C 383 ASP cc_start: 0.9064 (t0) cc_final: 0.8532 (m-30) REVERT: C 435 MET cc_start: 0.9044 (mmt) cc_final: 0.8150 (mmt) REVERT: C 442 MET cc_start: 0.9202 (tpp) cc_final: 0.8846 (mmm) REVERT: C 464 ASN cc_start: 0.8978 (t0) cc_final: 0.8613 (t0) REVERT: C 515 GLU cc_start: 0.7595 (tp30) cc_final: 0.7343 (mm-30) REVERT: C 528 MET cc_start: 0.8577 (tpp) cc_final: 0.8297 (tpp) REVERT: C 578 MET cc_start: 0.8130 (mmt) cc_final: 0.7632 (mmt) REVERT: C 587 HIS cc_start: 0.8825 (p-80) cc_final: 0.8284 (p-80) REVERT: C 590 ASP cc_start: 0.8694 (m-30) cc_final: 0.8045 (p0) REVERT: D 29 TRP cc_start: 0.6791 (t-100) cc_final: 0.6403 (t60) REVERT: D 66 LYS cc_start: 0.9474 (tppt) cc_final: 0.8994 (tptp) REVERT: D 92 LEU cc_start: 0.9439 (pp) cc_final: 0.9125 (pt) REVERT: D 122 HIS cc_start: 0.9448 (m90) cc_final: 0.8843 (m90) REVERT: D 178 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8751 (mm) REVERT: D 315 GLU cc_start: 0.9161 (tp30) cc_final: 0.8680 (tp30) REVERT: D 318 SER cc_start: 0.9747 (t) cc_final: 0.9460 (p) REVERT: D 331 MET cc_start: 0.8475 (tpp) cc_final: 0.7742 (tmm) REVERT: D 383 ASP cc_start: 0.8969 (t0) cc_final: 0.8445 (m-30) REVERT: D 402 VAL cc_start: 0.9090 (p) cc_final: 0.8349 (p) REVERT: D 435 MET cc_start: 0.8899 (mmt) cc_final: 0.8100 (mmt) REVERT: D 440 MET cc_start: 0.9046 (tpt) cc_final: 0.8805 (tpp) REVERT: D 444 LEU cc_start: 0.9578 (mp) cc_final: 0.9257 (mt) REVERT: D 466 MET cc_start: 0.9322 (mtt) cc_final: 0.8974 (mmt) REVERT: D 485 MET cc_start: 0.8251 (ttm) cc_final: 0.7652 (ttm) REVERT: D 554 MET cc_start: 0.8554 (tpt) cc_final: 0.8225 (tpt) REVERT: D 577 MET cc_start: 0.8476 (tpp) cc_final: 0.8102 (tpp) REVERT: D 578 MET cc_start: 0.8114 (mmt) cc_final: 0.7868 (mmt) REVERT: D 587 HIS cc_start: 0.8772 (p-80) cc_final: 0.8456 (p-80) REVERT: D 590 ASP cc_start: 0.8635 (m-30) cc_final: 0.8144 (p0) REVERT: D 603 MET cc_start: 0.8807 (ttt) cc_final: 0.8465 (tmm) REVERT: D 635 ASP cc_start: 0.8578 (t0) cc_final: 0.8182 (t0) outliers start: 57 outliers final: 25 residues processed: 434 average time/residue: 0.1061 time to fit residues: 75.5503 Evaluate side-chains 382 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 354 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 B residue 200 LEU 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 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 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 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: 7.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 28 optimal weight: 0.0060 chunk 112 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 546 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 197 ASN C 201 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS D 522 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.098554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076360 restraints weight = 55104.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079531 restraints weight = 26860.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081703 restraints weight = 16599.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083170 restraints weight = 11785.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.084149 restraints weight = 9270.048| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4280 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= 0.142 Angle : 0.706 11.933 27424 Z= 0.347 Chirality : 0.042 0.166 3102 Planarity : 0.004 0.061 3454 Dihedral : 9.321 88.450 2805 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.97 % Allowed : 15.52 % Favored : 81.51 % 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 aren not related in a simple way. whole: -2.26 (0.17), residues: 2436 helix: -0.49 (0.14), residues: 1372 sheet: -2.89 (0.57), residues: 68 loop : -2.86 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 584 TYR 0.018 0.001 TYR C 324 PHE 0.015 0.001 PHE C 162 TRP 0.009 0.001 TRP D 593 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00319 (20209) covalent geometry : angle 0.70552 (27424) hydrogen bonds : bond 0.03485 ( 760) hydrogen bonds : angle 4.53503 ( 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 435 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 372 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.9375 (m-30) cc_final: 0.9171 (m-30) REVERT: A 92 LEU cc_start: 0.9445 (pp) cc_final: 0.9242 (pp) REVERT: A 122 HIS cc_start: 0.9395 (m90) cc_final: 0.8683 (m90) REVERT: A 200 LEU cc_start: 0.9283 (mt) cc_final: 0.9013 (mt) REVERT: A 302 ARG cc_start: 0.8233 (tpm170) cc_final: 0.7430 (tpm170) REVERT: A 331 MET cc_start: 0.8540 (tpp) cc_final: 0.7576 (tmm) REVERT: A 383 ASP cc_start: 0.9090 (t0) cc_final: 0.8582 (m-30) REVERT: A 435 MET cc_start: 0.8843 (mmt) cc_final: 0.7879 (mmm) REVERT: A 444 LEU cc_start: 0.9506 (mp) cc_final: 0.9259 (mt) REVERT: A 466 MET cc_start: 0.9463 (mtt) cc_final: 0.9209 (mmt) REVERT: A 474 MET cc_start: 0.8793 (tpp) cc_final: 0.8564 (tpp) REVERT: A 515 GLU cc_start: 0.7315 (tp30) cc_final: 0.6824 (mm-30) REVERT: A 528 MET cc_start: 0.8452 (tpp) cc_final: 0.8108 (tpp) REVERT: A 635 ASP cc_start: 0.8597 (t0) cc_final: 0.8308 (t0) REVERT: B 122 HIS cc_start: 0.9370 (m90) cc_final: 0.8611 (m90) REVERT: B 176 GLU cc_start: 0.9381 (pm20) cc_final: 0.8969 (mp0) REVERT: B 177 GLU cc_start: 0.9366 (pm20) cc_final: 0.9052 (pm20) REVERT: B 200 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8870 (mt) REVERT: B 318 SER cc_start: 0.9784 (t) cc_final: 0.9537 (p) REVERT: B 383 ASP cc_start: 0.9043 (t0) cc_final: 0.8539 (m-30) REVERT: B 386 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 435 MET cc_start: 0.8910 (mmt) cc_final: 0.7970 (mmm) REVERT: B 442 MET cc_start: 0.9067 (tpp) cc_final: 0.8826 (mmm) REVERT: B 515 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7401 (mm-30) REVERT: B 528 MET cc_start: 0.8575 (tpp) cc_final: 0.8219 (tpp) REVERT: B 554 MET cc_start: 0.8436 (tpt) cc_final: 0.8143 (tpt) REVERT: B 577 MET cc_start: 0.8651 (tpp) cc_final: 0.8287 (tpp) REVERT: B 635 ASP cc_start: 0.8557 (t0) cc_final: 0.8271 (t0) REVERT: C 122 HIS cc_start: 0.9378 (m90) cc_final: 0.8645 (m90) REVERT: C 176 GLU cc_start: 0.9326 (pm20) cc_final: 0.9092 (mp0) REVERT: C 178 ILE cc_start: 0.9665 (mp) cc_final: 0.9279 (mp) REVERT: C 215 MET cc_start: 0.8860 (mmm) cc_final: 0.8526 (mmp) REVERT: C 302 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7426 (tpp-160) REVERT: C 318 SER cc_start: 0.9771 (t) cc_final: 0.9517 (p) REVERT: C 383 ASP cc_start: 0.9076 (t0) cc_final: 0.8599 (m-30) REVERT: C 435 MET cc_start: 0.8924 (mmt) cc_final: 0.8087 (mmm) REVERT: C 442 MET cc_start: 0.9141 (tpp) cc_final: 0.8805 (mmm) REVERT: C 515 GLU cc_start: 0.7496 (tp30) cc_final: 0.7024 (mm-30) REVERT: C 528 MET cc_start: 0.8637 (tpp) cc_final: 0.8297 (tpp) REVERT: C 577 MET cc_start: 0.8607 (tpp) cc_final: 0.8263 (tpp) REVERT: C 578 MET cc_start: 0.7981 (mmt) cc_final: 0.7714 (mmt) REVERT: C 635 ASP cc_start: 0.8452 (t0) cc_final: 0.8127 (t0) REVERT: D 92 LEU cc_start: 0.9357 (pp) cc_final: 0.9018 (pt) REVERT: D 99 MET cc_start: 0.8861 (mtp) cc_final: 0.8586 (ptp) REVERT: D 125 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9243 (p) REVERT: D 318 SER cc_start: 0.9748 (t) cc_final: 0.9469 (p) REVERT: D 331 MET cc_start: 0.8523 (tpp) cc_final: 0.7783 (tmm) REVERT: D 383 ASP cc_start: 0.8978 (t0) cc_final: 0.8465 (m-30) REVERT: D 435 MET cc_start: 0.8806 (mmt) cc_final: 0.7950 (mmm) REVERT: D 440 MET cc_start: 0.9172 (tpt) cc_final: 0.8920 (tpp) REVERT: D 444 LEU cc_start: 0.9560 (mp) cc_final: 0.9245 (mt) REVERT: D 466 MET cc_start: 0.9358 (mtt) cc_final: 0.9030 (mmt) REVERT: D 554 MET cc_start: 0.8575 (tpt) cc_final: 0.8203 (tpt) REVERT: D 577 MET cc_start: 0.8510 (tpp) cc_final: 0.8216 (tpp) REVERT: D 603 MET cc_start: 0.8892 (ttt) cc_final: 0.8430 (tmm) REVERT: D 635 ASP cc_start: 0.8522 (t0) cc_final: 0.8213 (t0) outliers start: 63 outliers final: 34 residues processed: 412 average time/residue: 0.1196 time to fit residues: 80.3162 Evaluate side-chains 381 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 344 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 386 LEU 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 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 499 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 125 VAL 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: 0.0070 chunk 31 optimal weight: 0.9990 chunk 231 optimal weight: 0.0170 chunk 78 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.100057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078122 restraints weight = 53912.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081315 restraints weight = 26475.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083490 restraints weight = 16335.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084972 restraints weight = 11590.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086048 restraints weight = 9073.768| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20209 Z= 0.115 Angle : 0.697 11.581 27424 Z= 0.339 Chirality : 0.042 0.167 3102 Planarity : 0.004 0.061 3454 Dihedral : 8.955 89.331 2805 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.22 % Allowed : 18.35 % Favored : 79.43 % 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 aren not related in a simple way. whole: -2.05 (0.17), residues: 2436 helix: -0.29 (0.14), residues: 1376 sheet: -2.82 (0.58), residues: 68 loop : -2.83 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 584 TYR 0.022 0.001 TYR C 324 PHE 0.010 0.001 PHE D 468 TRP 0.007 0.001 TRP C 613 HIS 0.006 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00258 (20209) covalent geometry : angle 0.69726 (27424) hydrogen bonds : bond 0.03205 ( 760) hydrogen bonds : angle 4.22210 ( 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 420 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6829 (t-100) cc_final: 0.6446 (t60) REVERT: A 122 HIS cc_start: 0.9344 (m90) cc_final: 0.8665 (m90) REVERT: A 176 GLU cc_start: 0.9383 (pm20) cc_final: 0.8948 (pm20) REVERT: A 200 LEU cc_start: 0.9256 (mt) cc_final: 0.8807 (mt) REVERT: A 290 GLN cc_start: 0.8543 (pm20) cc_final: 0.8039 (mm-40) REVERT: A 331 MET cc_start: 0.8535 (tpp) cc_final: 0.7584 (tmm) REVERT: A 383 ASP cc_start: 0.9046 (t0) cc_final: 0.8572 (m-30) REVERT: A 435 MET cc_start: 0.8861 (mmt) cc_final: 0.7877 (mmm) REVERT: A 444 LEU cc_start: 0.9519 (mp) cc_final: 0.9308 (mt) REVERT: A 466 MET cc_start: 0.9422 (mtt) cc_final: 0.9167 (mmt) REVERT: A 474 MET cc_start: 0.8807 (tpp) cc_final: 0.8602 (tpp) REVERT: A 515 GLU cc_start: 0.7337 (tp30) cc_final: 0.6906 (mm-30) REVERT: A 528 MET cc_start: 0.8352 (tpp) cc_final: 0.7928 (tpp) REVERT: A 635 ASP cc_start: 0.8583 (t0) cc_final: 0.8317 (t0) REVERT: B 29 TRP cc_start: 0.6706 (t-100) cc_final: 0.6420 (t60) REVERT: B 122 HIS cc_start: 0.9312 (m90) cc_final: 0.8612 (m90) REVERT: B 176 GLU cc_start: 0.9362 (pm20) cc_final: 0.9011 (mp0) REVERT: B 177 GLU cc_start: 0.9360 (pm20) cc_final: 0.9107 (pm20) REVERT: B 200 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8772 (mt) REVERT: B 232 LEU cc_start: 0.8481 (tt) cc_final: 0.8262 (tp) REVERT: B 302 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7398 (tpp-160) REVERT: B 318 SER cc_start: 0.9790 (t) cc_final: 0.9544 (p) REVERT: B 383 ASP cc_start: 0.9055 (t0) cc_final: 0.8564 (m-30) REVERT: B 435 MET cc_start: 0.8931 (mmt) cc_final: 0.7977 (mmm) REVERT: B 440 MET cc_start: 0.9370 (tpp) cc_final: 0.9066 (tmm) REVERT: B 442 MET cc_start: 0.9028 (tpp) cc_final: 0.8801 (mmm) REVERT: B 515 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 528 MET cc_start: 0.8408 (tpp) cc_final: 0.8025 (tpp) REVERT: B 551 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7698 (pp) REVERT: B 554 MET cc_start: 0.8496 (tpt) cc_final: 0.8258 (tpt) REVERT: B 577 MET cc_start: 0.8589 (tpp) cc_final: 0.8235 (tpp) REVERT: B 635 ASP cc_start: 0.8551 (t0) cc_final: 0.8260 (t0) REVERT: C 29 TRP cc_start: 0.6782 (t-100) cc_final: 0.6481 (t60) REVERT: C 122 HIS cc_start: 0.9323 (m90) cc_final: 0.8603 (m90) REVERT: C 173 VAL cc_start: 0.8562 (t) cc_final: 0.8325 (p) REVERT: C 176 GLU cc_start: 0.9446 (pm20) cc_final: 0.9088 (mp0) REVERT: C 177 GLU cc_start: 0.9184 (pm20) cc_final: 0.8763 (pm20) REVERT: C 178 ILE cc_start: 0.9512 (mp) cc_final: 0.9059 (mp) REVERT: C 215 MET cc_start: 0.8857 (mmm) cc_final: 0.8495 (mmp) REVERT: C 259 LEU cc_start: 0.9154 (tp) cc_final: 0.8876 (tt) REVERT: C 290 GLN cc_start: 0.8510 (pm20) cc_final: 0.7802 (mm-40) REVERT: C 302 ARG cc_start: 0.8101 (tpp-160) cc_final: 0.7761 (tpp-160) REVERT: C 318 SER cc_start: 0.9763 (t) cc_final: 0.9511 (p) REVERT: C 383 ASP cc_start: 0.9008 (t0) cc_final: 0.8469 (m-30) REVERT: C 435 MET cc_start: 0.8925 (mmt) cc_final: 0.8000 (mmm) REVERT: C 442 MET cc_start: 0.9079 (tpp) cc_final: 0.8714 (mmm) REVERT: C 528 MET cc_start: 0.8581 (tpp) cc_final: 0.8196 (tpp) REVERT: C 577 MET cc_start: 0.8539 (tpp) cc_final: 0.8098 (tpp) REVERT: C 635 ASP cc_start: 0.8449 (t0) cc_final: 0.8124 (t0) REVERT: D 29 TRP cc_start: 0.6738 (t-100) cc_final: 0.6339 (t60) REVERT: D 92 LEU cc_start: 0.9391 (pp) cc_final: 0.9190 (pt) REVERT: D 96 MET cc_start: 0.9318 (ptp) cc_final: 0.8898 (ptp) REVERT: D 99 MET cc_start: 0.8829 (mtp) cc_final: 0.8310 (ptp) REVERT: D 100 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8445 (mm-30) REVERT: D 177 GLU cc_start: 0.8935 (pm20) cc_final: 0.8393 (pp20) REVERT: D 178 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8876 (mp) REVERT: D 318 SER cc_start: 0.9751 (t) cc_final: 0.9475 (p) REVERT: D 331 MET cc_start: 0.8520 (tpp) cc_final: 0.7748 (tmm) REVERT: D 383 ASP cc_start: 0.8916 (t0) cc_final: 0.8411 (m-30) REVERT: D 435 MET cc_start: 0.8796 (mmt) cc_final: 0.8049 (mmt) REVERT: D 440 MET cc_start: 0.9139 (tpt) cc_final: 0.8852 (tmm) REVERT: D 444 LEU cc_start: 0.9567 (mp) cc_final: 0.9353 (mt) REVERT: D 466 MET cc_start: 0.9334 (mtt) cc_final: 0.9016 (mmt) REVERT: D 554 MET cc_start: 0.8518 (tpt) cc_final: 0.8143 (tpt) REVERT: D 603 MET cc_start: 0.8828 (ttt) cc_final: 0.8445 (tmm) REVERT: D 635 ASP cc_start: 0.8492 (t0) cc_final: 0.8195 (t0) outliers start: 47 outliers final: 31 residues processed: 405 average time/residue: 0.1209 time to fit residues: 79.0809 Evaluate side-chains 373 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 339 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 436 VAL 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 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 200 LEU 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 536 LEU Chi-restraints excluded: chain B residue 551 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 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 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 311 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 197 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 73 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 201 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN D 582 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.097996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075857 restraints weight = 54849.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079036 restraints weight = 27074.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081218 restraints weight = 16794.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082740 restraints weight = 11947.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083726 restraints weight = 9350.168| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20209 Z= 0.125 Angle : 0.705 14.567 27424 Z= 0.339 Chirality : 0.042 0.170 3102 Planarity : 0.004 0.055 3454 Dihedral : 8.474 89.370 2805 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.92 % Allowed : 18.92 % Favored : 78.16 % 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 aren not related in a simple way. whole: -1.85 (0.17), residues: 2436 helix: -0.11 (0.14), residues: 1384 sheet: -2.86 (0.59), residues: 68 loop : -2.78 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 180 TYR 0.020 0.001 TYR C 324 PHE 0.011 0.001 PHE A 211 TRP 0.008 0.001 TRP D 593 HIS 0.005 0.001 HIS C 587 Details of bonding type rmsd covalent geometry : bond 0.00287 (20209) covalent geometry : angle 0.70493 (27424) hydrogen bonds : bond 0.03108 ( 760) hydrogen bonds : angle 4.16907 ( 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 419 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 357 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6900 (t-100) cc_final: 0.6506 (t60) REVERT: A 122 HIS cc_start: 0.9317 (m90) cc_final: 0.8814 (m-70) REVERT: A 125 VAL cc_start: 0.9538 (t) cc_final: 0.9297 (p) REVERT: A 130 MET cc_start: 0.8722 (ptt) cc_final: 0.8335 (ptt) REVERT: A 176 GLU cc_start: 0.9380 (pm20) cc_final: 0.8957 (pm20) REVERT: A 200 LEU cc_start: 0.9207 (mt) cc_final: 0.8735 (mt) REVERT: A 290 GLN cc_start: 0.8503 (pm20) cc_final: 0.7977 (mm-40) REVERT: A 302 ARG cc_start: 0.8214 (tpm170) cc_final: 0.7823 (tpm170) REVERT: A 331 MET cc_start: 0.8527 (tpp) cc_final: 0.7596 (tmm) REVERT: A 383 ASP cc_start: 0.9118 (t0) cc_final: 0.8625 (m-30) REVERT: A 435 MET cc_start: 0.8765 (mmt) cc_final: 0.7787 (mmm) REVERT: A 444 LEU cc_start: 0.9498 (mp) cc_final: 0.9284 (mt) REVERT: A 454 MET cc_start: 0.8963 (tpt) cc_final: 0.8673 (tpt) REVERT: A 466 MET cc_start: 0.9477 (mtt) cc_final: 0.9190 (mmt) REVERT: A 474 MET cc_start: 0.8782 (tpp) cc_final: 0.8562 (tpp) REVERT: A 515 GLU cc_start: 0.7373 (tp30) cc_final: 0.6920 (mm-30) REVERT: A 528 MET cc_start: 0.8288 (tpp) cc_final: 0.7838 (tpp) REVERT: A 568 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 635 ASP cc_start: 0.8559 (t0) cc_final: 0.8239 (t0) REVERT: B 29 TRP cc_start: 0.6830 (t-100) cc_final: 0.6500 (t60) REVERT: B 113 GLU cc_start: 0.9464 (tt0) cc_final: 0.9113 (tp30) REVERT: B 122 HIS cc_start: 0.9295 (m90) cc_final: 0.8619 (m90) REVERT: B 125 VAL cc_start: 0.9544 (t) cc_final: 0.9329 (p) REVERT: B 200 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 242 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8912 (t) REVERT: B 302 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7496 (tpm170) REVERT: B 318 SER cc_start: 0.9774 (t) cc_final: 0.9517 (p) REVERT: B 383 ASP cc_start: 0.9090 (t0) cc_final: 0.8557 (m-30) REVERT: B 435 MET cc_start: 0.8831 (mmt) cc_final: 0.7937 (mmm) REVERT: B 440 MET cc_start: 0.9374 (tpp) cc_final: 0.9083 (tmm) REVERT: B 442 MET cc_start: 0.9005 (tpp) cc_final: 0.8751 (mmm) REVERT: B 528 MET cc_start: 0.8411 (tpp) cc_final: 0.7990 (tpp) REVERT: B 551 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7704 (pp) REVERT: B 554 MET cc_start: 0.8541 (tpt) cc_final: 0.8260 (tpt) REVERT: B 577 MET cc_start: 0.8573 (tpp) cc_final: 0.8217 (tpp) REVERT: B 635 ASP cc_start: 0.8525 (t0) cc_final: 0.8194 (t0) REVERT: C 51 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8292 (mt) REVERT: C 122 HIS cc_start: 0.9312 (m90) cc_final: 0.8830 (m-70) REVERT: C 125 VAL cc_start: 0.9646 (t) cc_final: 0.9442 (p) REVERT: C 176 GLU cc_start: 0.9437 (pm20) cc_final: 0.9121 (mp0) REVERT: C 177 GLU cc_start: 0.9264 (pm20) cc_final: 0.8889 (pm20) REVERT: C 178 ILE cc_start: 0.9554 (mp) cc_final: 0.9164 (mp) REVERT: C 215 MET cc_start: 0.8905 (mmm) cc_final: 0.8522 (mmp) REVERT: C 259 LEU cc_start: 0.9131 (tp) cc_final: 0.8853 (tt) REVERT: C 302 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7642 (tpp-160) REVERT: C 318 SER cc_start: 0.9763 (t) cc_final: 0.9502 (p) REVERT: C 383 ASP cc_start: 0.9065 (t0) cc_final: 0.8655 (m-30) REVERT: C 435 MET cc_start: 0.8876 (mmt) cc_final: 0.7865 (mmm) REVERT: C 515 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7210 (mm-30) REVERT: C 528 MET cc_start: 0.8595 (tpp) cc_final: 0.8184 (tpp) REVERT: C 577 MET cc_start: 0.8552 (tpp) cc_final: 0.8125 (tpp) REVERT: C 635 ASP cc_start: 0.8470 (t0) cc_final: 0.8157 (t0) REVERT: D 29 TRP cc_start: 0.6813 (t-100) cc_final: 0.6393 (t60) REVERT: D 66 LYS cc_start: 0.9151 (mttt) cc_final: 0.8932 (mttp) REVERT: D 92 LEU cc_start: 0.9385 (pp) cc_final: 0.9105 (pt) REVERT: D 96 MET cc_start: 0.9342 (ptp) cc_final: 0.8925 (ptp) REVERT: D 99 MET cc_start: 0.8934 (mtp) cc_final: 0.8396 (ptp) REVERT: D 100 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8537 (mm-30) REVERT: D 177 GLU cc_start: 0.9094 (pm20) cc_final: 0.8683 (pm20) REVERT: D 178 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8564 (mm) REVERT: D 315 GLU cc_start: 0.9251 (tp30) cc_final: 0.8773 (tp30) REVERT: D 318 SER cc_start: 0.9743 (t) cc_final: 0.9460 (p) REVERT: D 331 MET cc_start: 0.8503 (tpp) cc_final: 0.7748 (tmm) REVERT: D 383 ASP cc_start: 0.8945 (t0) cc_final: 0.8418 (m-30) REVERT: D 390 LEU cc_start: 0.9391 (mm) cc_final: 0.9151 (mm) REVERT: D 435 MET cc_start: 0.8744 (mmt) cc_final: 0.7813 (mmt) REVERT: D 440 MET cc_start: 0.9235 (tpt) cc_final: 0.8972 (tmm) REVERT: D 466 MET cc_start: 0.9382 (mtt) cc_final: 0.9064 (mmm) REVERT: D 554 MET cc_start: 0.8575 (tpt) cc_final: 0.8189 (tpt) REVERT: D 603 MET cc_start: 0.8791 (ttt) cc_final: 0.8401 (tmm) REVERT: D 635 ASP cc_start: 0.8533 (t0) cc_final: 0.8233 (t0) outliers start: 62 outliers final: 39 residues processed: 395 average time/residue: 0.1099 time to fit residues: 71.6448 Evaluate side-chains 395 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 403 GLU 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 200 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 436 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 238 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 242 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 0.7952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.101056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079057 restraints weight = 53828.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082302 restraints weight = 26342.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084535 restraints weight = 16193.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086063 restraints weight = 11444.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.087064 restraints weight = 8902.600| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20209 Z= 0.111 Angle : 0.711 12.274 27424 Z= 0.338 Chirality : 0.041 0.170 3102 Planarity : 0.004 0.053 3454 Dihedral : 7.898 86.677 2805 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.17 % Allowed : 20.71 % Favored : 77.12 % 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 aren not related in a simple way. whole: -1.72 (0.17), residues: 2436 helix: 0.02 (0.14), residues: 1380 sheet: -2.77 (0.59), residues: 68 loop : -2.76 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 75 TYR 0.021 0.001 TYR C 324 PHE 0.008 0.001 PHE D 468 TRP 0.008 0.001 TRP B 629 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00254 (20209) covalent geometry : angle 0.71098 (27424) hydrogen bonds : bond 0.02942 ( 760) hydrogen bonds : angle 4.04333 ( 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 409 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6864 (t-100) cc_final: 0.6483 (t60) REVERT: A 96 MET cc_start: 0.9252 (ppp) cc_final: 0.9051 (ppp) REVERT: A 99 MET cc_start: 0.9262 (ptp) cc_final: 0.8609 (ptm) REVERT: A 113 GLU cc_start: 0.9457 (tt0) cc_final: 0.9100 (tp30) REVERT: A 122 HIS cc_start: 0.9361 (m90) cc_final: 0.8832 (m-70) REVERT: A 125 VAL cc_start: 0.9539 (t) cc_final: 0.9296 (p) REVERT: A 130 MET cc_start: 0.8554 (ptt) cc_final: 0.8146 (ptt) REVERT: A 177 GLU cc_start: 0.9388 (pm20) cc_final: 0.9178 (pm20) REVERT: A 200 LEU cc_start: 0.9183 (mt) cc_final: 0.8709 (mt) REVERT: A 290 GLN cc_start: 0.8447 (pm20) cc_final: 0.7940 (mm-40) REVERT: A 302 ARG cc_start: 0.8254 (tpm170) cc_final: 0.7799 (tpm170) REVERT: A 331 MET cc_start: 0.8505 (tpp) cc_final: 0.7564 (tmm) REVERT: A 383 ASP cc_start: 0.9099 (t0) cc_final: 0.8589 (m-30) REVERT: A 435 MET cc_start: 0.8708 (mmt) cc_final: 0.7767 (mmm) REVERT: A 466 MET cc_start: 0.9420 (mtt) cc_final: 0.9183 (mmt) REVERT: A 474 MET cc_start: 0.8773 (tpp) cc_final: 0.8539 (tpp) REVERT: A 515 GLU cc_start: 0.7340 (tp30) cc_final: 0.6885 (mm-30) REVERT: A 528 MET cc_start: 0.8274 (tpp) cc_final: 0.7806 (tpp) REVERT: A 568 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 608 LEU cc_start: 0.9350 (mp) cc_final: 0.9006 (tt) REVERT: A 635 ASP cc_start: 0.8602 (t0) cc_final: 0.8346 (t0) REVERT: B 29 TRP cc_start: 0.6722 (t-100) cc_final: 0.6434 (t60) REVERT: B 96 MET cc_start: 0.9293 (ppp) cc_final: 0.8978 (ppp) REVERT: B 113 GLU cc_start: 0.9442 (tt0) cc_final: 0.9089 (tp30) REVERT: B 122 HIS cc_start: 0.9305 (m90) cc_final: 0.8845 (m-70) REVERT: B 125 VAL cc_start: 0.9527 (t) cc_final: 0.9312 (p) REVERT: B 176 GLU cc_start: 0.9470 (pm20) cc_final: 0.9044 (pm20) REVERT: B 200 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8715 (mt) REVERT: B 242 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8914 (t) REVERT: B 290 GLN cc_start: 0.8508 (pm20) cc_final: 0.7764 (mm-40) REVERT: B 302 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7472 (tpm170) REVERT: B 318 SER cc_start: 0.9768 (t) cc_final: 0.9511 (p) REVERT: B 383 ASP cc_start: 0.9087 (t0) cc_final: 0.8539 (m-30) REVERT: B 435 MET cc_start: 0.8827 (mmt) cc_final: 0.7928 (mmm) REVERT: B 440 MET cc_start: 0.9361 (tpp) cc_final: 0.9107 (tmm) REVERT: B 442 MET cc_start: 0.9001 (tpp) cc_final: 0.8750 (mmm) REVERT: B 528 MET cc_start: 0.8421 (tpp) cc_final: 0.7986 (tpp) REVERT: B 554 MET cc_start: 0.8454 (tpt) cc_final: 0.8189 (tpt) REVERT: B 577 MET cc_start: 0.8461 (tpp) cc_final: 0.8077 (tpp) REVERT: B 608 LEU cc_start: 0.9332 (mp) cc_final: 0.8983 (tt) REVERT: B 635 ASP cc_start: 0.8585 (t0) cc_final: 0.8318 (t0) REVERT: C 29 TRP cc_start: 0.6784 (t-100) cc_final: 0.6475 (t60) REVERT: C 51 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (mt) REVERT: C 113 GLU cc_start: 0.9440 (tt0) cc_final: 0.9100 (tp30) REVERT: C 118 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: C 122 HIS cc_start: 0.9318 (m90) cc_final: 0.8789 (m-70) REVERT: C 125 VAL cc_start: 0.9629 (t) cc_final: 0.9382 (p) REVERT: C 173 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 176 GLU cc_start: 0.9429 (pm20) cc_final: 0.8982 (mp0) REVERT: C 177 GLU cc_start: 0.9287 (pm20) cc_final: 0.8957 (pm20) REVERT: C 178 ILE cc_start: 0.9569 (mp) cc_final: 0.9195 (mm) REVERT: C 215 MET cc_start: 0.8888 (mmm) cc_final: 0.8302 (mmp) REVERT: C 242 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8946 (t) REVERT: C 259 LEU cc_start: 0.9115 (tp) cc_final: 0.8822 (tt) REVERT: C 290 GLN cc_start: 0.8485 (pm20) cc_final: 0.7810 (mm-40) REVERT: C 302 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7672 (tpp-160) REVERT: C 318 SER cc_start: 0.9760 (t) cc_final: 0.9498 (p) REVERT: C 383 ASP cc_start: 0.9075 (t0) cc_final: 0.8512 (m-30) REVERT: C 435 MET cc_start: 0.8835 (mmt) cc_final: 0.7866 (mmm) REVERT: C 454 MET cc_start: 0.9045 (tpp) cc_final: 0.8835 (tpp) REVERT: C 464 ASN cc_start: 0.8907 (t0) cc_final: 0.8391 (t0) REVERT: C 528 MET cc_start: 0.8569 (tpp) cc_final: 0.8180 (tpp) REVERT: C 577 MET cc_start: 0.8468 (tpp) cc_final: 0.8229 (tpp) REVERT: C 635 ASP cc_start: 0.8466 (t0) cc_final: 0.8143 (t0) REVERT: D 29 TRP cc_start: 0.6859 (t-100) cc_final: 0.6452 (t60) REVERT: D 66 LYS cc_start: 0.9157 (mttt) cc_final: 0.8923 (mttp) REVERT: D 92 LEU cc_start: 0.9403 (pp) cc_final: 0.9103 (pt) REVERT: D 96 MET cc_start: 0.9340 (ptp) cc_final: 0.8860 (ptp) REVERT: D 99 MET cc_start: 0.8924 (mtp) cc_final: 0.8417 (ptm) REVERT: D 100 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8547 (mm-30) REVERT: D 125 VAL cc_start: 0.9360 (t) cc_final: 0.9132 (p) REVERT: D 177 GLU cc_start: 0.9154 (pm20) cc_final: 0.8748 (pm20) REVERT: D 178 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8578 (mm) REVERT: D 302 ARG cc_start: 0.8104 (tpm170) cc_final: 0.7658 (tpm170) REVERT: D 315 GLU cc_start: 0.9253 (tp30) cc_final: 0.8777 (tp30) REVERT: D 318 SER cc_start: 0.9737 (t) cc_final: 0.9457 (p) REVERT: D 331 MET cc_start: 0.8476 (tpp) cc_final: 0.7745 (tmm) REVERT: D 383 ASP cc_start: 0.8927 (t0) cc_final: 0.8419 (m-30) REVERT: D 435 MET cc_start: 0.8702 (mmt) cc_final: 0.7755 (mmt) REVERT: D 440 MET cc_start: 0.9220 (tpt) cc_final: 0.9012 (tmm) REVERT: D 466 MET cc_start: 0.9395 (mtt) cc_final: 0.9024 (mmm) REVERT: D 554 MET cc_start: 0.8532 (tpt) cc_final: 0.8146 (tpt) REVERT: D 603 MET cc_start: 0.8805 (ttt) cc_final: 0.8419 (tmm) REVERT: D 635 ASP cc_start: 0.8533 (t0) cc_final: 0.8229 (t0) outliers start: 46 outliers final: 29 residues processed: 392 average time/residue: 0.1191 time to fit residues: 75.9426 Evaluate side-chains 384 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 347 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 403 GLU 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 B residue 200 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 479 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 118 GLN 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 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 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 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: 0.9980 chunk 1 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 130 optimal weight: 0.0030 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076015 restraints weight = 55411.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079314 restraints weight = 26976.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081565 restraints weight = 16596.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083136 restraints weight = 11748.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084200 restraints weight = 9157.687| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20209 Z= 0.124 Angle : 0.715 12.167 27424 Z= 0.342 Chirality : 0.042 0.177 3102 Planarity : 0.004 0.056 3454 Dihedral : 7.569 88.573 2805 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % Favored : 77.36 % 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 aren not related in a simple way. whole: -1.58 (0.17), residues: 2436 helix: 0.11 (0.14), residues: 1384 sheet: -2.75 (0.60), residues: 68 loop : -2.65 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 385 TYR 0.021 0.001 TYR C 324 PHE 0.010 0.001 PHE B 211 TRP 0.009 0.001 TRP A 629 HIS 0.005 0.001 HIS C 587 Details of bonding type rmsd covalent geometry : bond 0.00289 (20209) covalent geometry : angle 0.71496 (27424) hydrogen bonds : bond 0.02912 ( 760) hydrogen bonds : angle 4.10120 ( 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 420 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6815 (t-100) cc_final: 0.6467 (t60) REVERT: A 113 GLU cc_start: 0.9422 (tt0) cc_final: 0.9080 (tp30) REVERT: A 122 HIS cc_start: 0.9299 (m90) cc_final: 0.8520 (m90) REVERT: A 125 VAL cc_start: 0.9595 (t) cc_final: 0.9360 (p) REVERT: A 130 MET cc_start: 0.8522 (ptt) cc_final: 0.8121 (ptt) REVERT: A 176 GLU cc_start: 0.9290 (pm20) cc_final: 0.9064 (pm20) REVERT: A 200 LEU cc_start: 0.9236 (mt) cc_final: 0.8779 (mt) REVERT: A 242 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8961 (t) REVERT: A 290 GLN cc_start: 0.8407 (pm20) cc_final: 0.7899 (mm-40) REVERT: A 302 ARG cc_start: 0.8312 (tpm170) cc_final: 0.7869 (tpm170) REVERT: A 331 MET cc_start: 0.8513 (tpp) cc_final: 0.7579 (tmm) REVERT: A 383 ASP cc_start: 0.9089 (t0) cc_final: 0.8616 (m-30) REVERT: A 435 MET cc_start: 0.8751 (mmt) cc_final: 0.7733 (mmt) REVERT: A 466 MET cc_start: 0.9405 (mtt) cc_final: 0.9160 (mmt) REVERT: A 515 GLU cc_start: 0.7413 (tp30) cc_final: 0.6946 (mm-30) REVERT: A 528 MET cc_start: 0.8469 (tpp) cc_final: 0.7986 (tpp) REVERT: A 608 LEU cc_start: 0.9355 (mp) cc_final: 0.9009 (tt) REVERT: A 635 ASP cc_start: 0.8622 (t0) cc_final: 0.8351 (t0) REVERT: B 29 TRP cc_start: 0.6716 (t-100) cc_final: 0.6450 (t60) REVERT: B 113 GLU cc_start: 0.9426 (tt0) cc_final: 0.9077 (tp30) REVERT: B 122 HIS cc_start: 0.9281 (m90) cc_final: 0.8825 (m-70) REVERT: B 125 VAL cc_start: 0.9560 (t) cc_final: 0.9355 (p) REVERT: B 200 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 242 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8956 (t) REVERT: B 290 GLN cc_start: 0.8542 (pm20) cc_final: 0.7774 (mm-40) REVERT: B 302 ARG cc_start: 0.8019 (tpp-160) cc_final: 0.7561 (tpm170) REVERT: B 318 SER cc_start: 0.9783 (t) cc_final: 0.9523 (p) REVERT: B 383 ASP cc_start: 0.9074 (t0) cc_final: 0.8551 (m-30) REVERT: B 435 MET cc_start: 0.8823 (mmt) cc_final: 0.7856 (mmm) REVERT: B 440 MET cc_start: 0.9365 (tpp) cc_final: 0.9111 (tmm) REVERT: B 442 MET cc_start: 0.9001 (tpp) cc_final: 0.8751 (mmm) REVERT: B 528 MET cc_start: 0.8515 (tpp) cc_final: 0.8067 (tpp) REVERT: B 554 MET cc_start: 0.8452 (tpt) cc_final: 0.8198 (tpt) REVERT: B 577 MET cc_start: 0.8438 (tpp) cc_final: 0.8150 (tpp) REVERT: B 608 LEU cc_start: 0.9331 (mp) cc_final: 0.8987 (tt) REVERT: B 635 ASP cc_start: 0.8615 (t0) cc_final: 0.8334 (t0) REVERT: C 29 TRP cc_start: 0.6767 (t-100) cc_final: 0.6489 (t60) REVERT: C 51 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8308 (mt) REVERT: C 113 GLU cc_start: 0.9422 (tt0) cc_final: 0.9091 (tp30) REVERT: C 118 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: C 122 HIS cc_start: 0.9270 (m90) cc_final: 0.8702 (m-70) REVERT: C 125 VAL cc_start: 0.9648 (t) cc_final: 0.9413 (p) REVERT: C 173 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 177 GLU cc_start: 0.9293 (pm20) cc_final: 0.9084 (pm20) REVERT: C 178 ILE cc_start: 0.9563 (mp) cc_final: 0.9261 (mm) REVERT: C 215 MET cc_start: 0.8812 (mmm) cc_final: 0.8569 (mmp) REVERT: C 242 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8986 (t) REVERT: C 259 LEU cc_start: 0.9081 (tp) cc_final: 0.8829 (tt) REVERT: C 290 GLN cc_start: 0.8515 (pm20) cc_final: 0.7813 (mm-40) REVERT: C 302 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7715 (tpp-160) REVERT: C 318 SER cc_start: 0.9780 (t) cc_final: 0.9513 (p) REVERT: C 383 ASP cc_start: 0.9033 (t0) cc_final: 0.8653 (m-30) REVERT: C 435 MET cc_start: 0.8941 (mmt) cc_final: 0.7964 (mmm) REVERT: C 515 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6829 (mm-30) REVERT: C 528 MET cc_start: 0.8674 (tpp) cc_final: 0.8278 (tpp) REVERT: C 577 MET cc_start: 0.8515 (tpp) cc_final: 0.8144 (tpp) REVERT: C 635 ASP cc_start: 0.8517 (t0) cc_final: 0.8227 (t0) REVERT: D 29 TRP cc_start: 0.6889 (t-100) cc_final: 0.6490 (t60) REVERT: D 66 LYS cc_start: 0.9145 (mttt) cc_final: 0.8904 (mttp) REVERT: D 92 LEU cc_start: 0.9385 (pp) cc_final: 0.9056 (pt) REVERT: D 96 MET cc_start: 0.9329 (ptp) cc_final: 0.8811 (ptp) REVERT: D 99 MET cc_start: 0.8940 (mtp) cc_final: 0.8414 (ptm) REVERT: D 100 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8555 (mm-30) REVERT: D 177 GLU cc_start: 0.9204 (pm20) cc_final: 0.8856 (pm20) REVERT: D 178 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.8865 (mm) REVERT: D 260 MET cc_start: 0.8848 (mmm) cc_final: 0.8634 (tpp) REVERT: D 290 GLN cc_start: 0.8405 (pm20) cc_final: 0.7512 (mm-40) REVERT: D 302 ARG cc_start: 0.8127 (tpm170) cc_final: 0.7671 (tpm170) REVERT: D 318 SER cc_start: 0.9753 (t) cc_final: 0.9490 (p) REVERT: D 331 MET cc_start: 0.8497 (tpp) cc_final: 0.7738 (tmm) REVERT: D 383 ASP cc_start: 0.8999 (t0) cc_final: 0.8594 (m-30) REVERT: D 435 MET cc_start: 0.8783 (mmt) cc_final: 0.7844 (mmt) REVERT: D 445 ILE cc_start: 0.9566 (tp) cc_final: 0.9347 (pt) REVERT: D 466 MET cc_start: 0.9388 (mtt) cc_final: 0.9027 (mmm) REVERT: D 554 MET cc_start: 0.8559 (tpt) cc_final: 0.8200 (tpt) REVERT: D 577 MET cc_start: 0.8112 (tpp) cc_final: 0.7737 (tpp) REVERT: D 587 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8426 (t70) REVERT: D 603 MET cc_start: 0.8820 (ttt) cc_final: 0.8460 (tmm) REVERT: D 635 ASP cc_start: 0.8569 (t0) cc_final: 0.8291 (t0) outliers start: 56 outliers final: 31 residues processed: 399 average time/residue: 0.1181 time to fit residues: 77.7501 Evaluate side-chains 391 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 403 GLU 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 200 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 B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 118 GLN 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 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 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 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: 0.9980 chunk 71 optimal weight: 0.1980 chunk 73 optimal weight: 0.0670 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.101514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079858 restraints weight = 53246.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083076 restraints weight = 26397.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085280 restraints weight = 16347.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.086820 restraints weight = 11574.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.087819 restraints weight = 9012.069| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5455 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= 0.117 Angle : 0.757 11.750 27424 Z= 0.358 Chirality : 0.043 0.234 3102 Planarity : 0.004 0.049 3454 Dihedral : 7.158 88.295 2805 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.89 % Allowed : 21.46 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.17), residues: 2436 helix: 0.10 (0.14), residues: 1384 sheet: -2.68 (0.60), residues: 68 loop : -2.64 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.023 0.001 TYR C 324 PHE 0.010 0.001 PHE A 211 TRP 0.008 0.001 TRP A 629 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00270 (20209) covalent geometry : angle 0.75669 (27424) hydrogen bonds : bond 0.02904 ( 760) hydrogen bonds : angle 4.07421 ( 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 407 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 367 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6750 (t-100) cc_final: 0.6431 (t60) REVERT: A 99 MET cc_start: 0.8429 (ptm) cc_final: 0.8209 (ptp) REVERT: A 113 GLU cc_start: 0.9354 (tt0) cc_final: 0.9042 (tp30) REVERT: A 122 HIS cc_start: 0.9290 (m90) cc_final: 0.8521 (m90) REVERT: A 125 VAL cc_start: 0.9574 (t) cc_final: 0.9336 (p) REVERT: A 130 MET cc_start: 0.8332 (ptt) cc_final: 0.7993 (ptt) REVERT: A 176 GLU cc_start: 0.9349 (pm20) cc_final: 0.8749 (pm20) REVERT: A 200 LEU cc_start: 0.9200 (mt) cc_final: 0.8734 (mt) REVERT: A 242 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8923 (t) REVERT: A 290 GLN cc_start: 0.8395 (pm20) cc_final: 0.7940 (mm-40) REVERT: A 302 ARG cc_start: 0.8349 (tpm170) cc_final: 0.7880 (tpm170) REVERT: A 331 MET cc_start: 0.8499 (tpp) cc_final: 0.7562 (tmm) REVERT: A 383 ASP cc_start: 0.9055 (t0) cc_final: 0.8571 (m-30) REVERT: A 435 MET cc_start: 0.8760 (mmt) cc_final: 0.7740 (mmt) REVERT: A 440 MET cc_start: 0.9356 (tpp) cc_final: 0.9147 (tmm) REVERT: A 466 MET cc_start: 0.9360 (mtt) cc_final: 0.9120 (mmt) REVERT: A 515 GLU cc_start: 0.7326 (tp30) cc_final: 0.6904 (mm-30) REVERT: A 528 MET cc_start: 0.8444 (tpp) cc_final: 0.7945 (tpp) REVERT: A 568 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 608 LEU cc_start: 0.9330 (mp) cc_final: 0.8982 (tt) REVERT: A 635 ASP cc_start: 0.8607 (t0) cc_final: 0.8316 (t0) REVERT: B 29 TRP cc_start: 0.6674 (t-100) cc_final: 0.6421 (t60) REVERT: B 78 MET cc_start: 0.7553 (pmm) cc_final: 0.7275 (pmm) REVERT: B 113 GLU cc_start: 0.9342 (tt0) cc_final: 0.9025 (tp30) REVERT: B 122 HIS cc_start: 0.9251 (m90) cc_final: 0.8795 (m-70) REVERT: B 125 VAL cc_start: 0.9543 (t) cc_final: 0.9338 (p) REVERT: B 200 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 242 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8927 (t) REVERT: B 290 GLN cc_start: 0.8353 (pm20) cc_final: 0.7548 (mm-40) REVERT: B 302 ARG cc_start: 0.8080 (tpp-160) cc_final: 0.7630 (tpm170) REVERT: B 318 SER cc_start: 0.9780 (t) cc_final: 0.9517 (p) REVERT: B 383 ASP cc_start: 0.9044 (t0) cc_final: 0.8539 (m-30) REVERT: B 435 MET cc_start: 0.8832 (mmt) cc_final: 0.7813 (mmm) REVERT: B 440 MET cc_start: 0.9330 (tpp) cc_final: 0.9093 (tmm) REVERT: B 442 MET cc_start: 0.8973 (tpp) cc_final: 0.8741 (mmm) REVERT: B 515 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6941 (mp0) REVERT: B 528 MET cc_start: 0.8491 (tpp) cc_final: 0.7988 (tpp) REVERT: B 554 MET cc_start: 0.8361 (tpt) cc_final: 0.8127 (tpt) REVERT: B 577 MET cc_start: 0.8519 (tpp) cc_final: 0.8166 (tpp) REVERT: B 608 LEU cc_start: 0.9321 (mp) cc_final: 0.8968 (tt) REVERT: B 635 ASP cc_start: 0.8629 (t0) cc_final: 0.8337 (t0) REVERT: C 29 TRP cc_start: 0.6680 (t-100) cc_final: 0.6434 (t60) REVERT: C 51 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 113 GLU cc_start: 0.9332 (tt0) cc_final: 0.9073 (tp30) REVERT: C 118 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: C 122 HIS cc_start: 0.9279 (m90) cc_final: 0.8742 (m-70) REVERT: C 125 VAL cc_start: 0.9619 (t) cc_final: 0.9393 (p) REVERT: C 173 VAL cc_start: 0.8346 (t) cc_final: 0.8074 (p) REVERT: C 177 GLU cc_start: 0.9223 (pm20) cc_final: 0.8930 (pm20) REVERT: C 178 ILE cc_start: 0.9545 (mp) cc_final: 0.9002 (mm) REVERT: C 242 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8964 (t) REVERT: C 259 LEU cc_start: 0.9036 (tp) cc_final: 0.8745 (tt) REVERT: C 290 GLN cc_start: 0.8345 (pm20) cc_final: 0.7645 (mm-40) REVERT: C 302 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7724 (tpp-160) REVERT: C 318 SER cc_start: 0.9781 (t) cc_final: 0.9516 (p) REVERT: C 383 ASP cc_start: 0.9040 (t0) cc_final: 0.8496 (m-30) REVERT: C 435 MET cc_start: 0.8938 (mmt) cc_final: 0.8103 (mmt) REVERT: C 464 ASN cc_start: 0.8860 (t0) cc_final: 0.8369 (t0) REVERT: C 515 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6761 (mm-30) REVERT: C 528 MET cc_start: 0.8556 (tpp) cc_final: 0.8077 (tpp) REVERT: C 577 MET cc_start: 0.8530 (tpp) cc_final: 0.8284 (tpp) REVERT: C 587 HIS cc_start: 0.8594 (p-80) cc_final: 0.8126 (t70) REVERT: C 608 LEU cc_start: 0.9311 (mp) cc_final: 0.8941 (tt) REVERT: C 635 ASP cc_start: 0.8501 (t0) cc_final: 0.8200 (t0) REVERT: D 29 TRP cc_start: 0.6806 (t-100) cc_final: 0.6448 (t60) REVERT: D 66 LYS cc_start: 0.9115 (mttt) cc_final: 0.8862 (mttp) REVERT: D 92 LEU cc_start: 0.9386 (pp) cc_final: 0.9052 (pt) REVERT: D 96 MET cc_start: 0.9321 (ptp) cc_final: 0.8793 (ptp) REVERT: D 99 MET cc_start: 0.8902 (mtp) cc_final: 0.8373 (ptm) REVERT: D 100 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8568 (mm-30) REVERT: D 125 VAL cc_start: 0.9365 (t) cc_final: 0.9149 (p) REVERT: D 177 GLU cc_start: 0.9181 (pm20) cc_final: 0.8750 (pm20) REVERT: D 178 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8538 (mm) REVERT: D 215 MET cc_start: 0.9102 (mmt) cc_final: 0.8833 (mmp) REVERT: D 260 MET cc_start: 0.8911 (mmm) cc_final: 0.8695 (tpp) REVERT: D 290 GLN cc_start: 0.8299 (pm20) cc_final: 0.7353 (mm-40) REVERT: D 302 ARG cc_start: 0.8178 (tpm170) cc_final: 0.7698 (tpm170) REVERT: D 318 SER cc_start: 0.9761 (t) cc_final: 0.9503 (p) REVERT: D 331 MET cc_start: 0.8432 (tpp) cc_final: 0.7702 (tmm) REVERT: D 383 ASP cc_start: 0.8979 (t0) cc_final: 0.8539 (m-30) REVERT: D 390 LEU cc_start: 0.9425 (mm) cc_final: 0.9172 (mm) REVERT: D 435 MET cc_start: 0.8779 (mmt) cc_final: 0.7822 (mmt) REVERT: D 466 MET cc_start: 0.9358 (mtt) cc_final: 0.8954 (mmm) REVERT: D 554 MET cc_start: 0.8485 (tpt) cc_final: 0.8148 (tpt) REVERT: D 587 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8368 (t70) REVERT: D 603 MET cc_start: 0.8816 (ttt) cc_final: 0.8452 (tmm) REVERT: D 608 LEU cc_start: 0.9369 (mp) cc_final: 0.9072 (tt) REVERT: D 635 ASP cc_start: 0.8551 (t0) cc_final: 0.8228 (t0) outliers start: 40 outliers final: 23 residues processed: 394 average time/residue: 0.1172 time to fit residues: 76.0949 Evaluate side-chains 388 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 403 GLU 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 B residue 200 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 51 LEU Chi-restraints excluded: chain C residue 118 GLN 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 440 MET 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 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 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: 7.9990 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.098381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076295 restraints weight = 53690.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079432 restraints weight = 26569.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081581 restraints weight = 16520.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083041 restraints weight = 11762.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084070 restraints weight = 9251.341| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20209 Z= 0.177 Angle : 0.795 12.438 27424 Z= 0.384 Chirality : 0.045 0.205 3102 Planarity : 0.004 0.045 3454 Dihedral : 7.185 79.247 2805 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 1.79 % Allowed : 21.70 % Favored : 76.51 % 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 aren not related in a simple way. whole: -1.51 (0.18), residues: 2436 helix: 0.13 (0.14), residues: 1388 sheet: -2.65 (0.61), residues: 68 loop : -2.57 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 385 TYR 0.022 0.001 TYR C 324 PHE 0.014 0.001 PHE C 162 TRP 0.012 0.001 TRP A 629 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00407 (20209) covalent geometry : angle 0.79470 (27424) hydrogen bonds : bond 0.03091 ( 760) hydrogen bonds : angle 4.42508 ( 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 388 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 350 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6790 (t-100) cc_final: 0.6453 (t60) REVERT: A 99 MET cc_start: 0.8482 (ptm) cc_final: 0.8255 (ptp) REVERT: A 113 GLU cc_start: 0.9402 (tt0) cc_final: 0.9047 (tp30) REVERT: A 125 VAL cc_start: 0.9627 (t) cc_final: 0.9407 (p) REVERT: A 130 MET cc_start: 0.8598 (ptt) cc_final: 0.8122 (ptt) REVERT: A 200 LEU cc_start: 0.9276 (mt) cc_final: 0.8808 (mt) REVERT: A 242 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8997 (t) REVERT: A 302 ARG cc_start: 0.8331 (tpm170) cc_final: 0.7871 (tpm170) REVERT: A 331 MET cc_start: 0.8552 (tpp) cc_final: 0.7653 (tmm) REVERT: A 383 ASP cc_start: 0.9079 (t0) cc_final: 0.8567 (m-30) REVERT: A 435 MET cc_start: 0.8830 (mmt) cc_final: 0.7837 (mmt) REVERT: A 440 MET cc_start: 0.9346 (tpp) cc_final: 0.9141 (tmm) REVERT: A 466 MET cc_start: 0.9439 (mtt) cc_final: 0.9164 (mmt) REVERT: A 515 GLU cc_start: 0.7453 (tp30) cc_final: 0.6981 (mm-30) REVERT: A 528 MET cc_start: 0.8712 (tpp) cc_final: 0.8298 (tpp) REVERT: A 608 LEU cc_start: 0.9386 (mp) cc_final: 0.9087 (tt) REVERT: A 635 ASP cc_start: 0.8612 (t0) cc_final: 0.8344 (t0) REVERT: B 29 TRP cc_start: 0.6690 (t-100) cc_final: 0.6440 (t60) REVERT: B 99 MET cc_start: 0.9087 (ptp) cc_final: 0.8653 (ptt) REVERT: B 113 GLU cc_start: 0.9380 (tt0) cc_final: 0.9042 (tp30) REVERT: B 242 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.9005 (t) REVERT: B 302 ARG cc_start: 0.8165 (tpp-160) cc_final: 0.7874 (tpm170) REVERT: B 318 SER cc_start: 0.9794 (t) cc_final: 0.9538 (p) REVERT: B 383 ASP cc_start: 0.9037 (t0) cc_final: 0.8541 (m-30) REVERT: B 435 MET cc_start: 0.8897 (mmt) cc_final: 0.7920 (mmm) REVERT: B 440 MET cc_start: 0.9326 (tpp) cc_final: 0.9095 (tmm) REVERT: B 442 MET cc_start: 0.9016 (tpp) cc_final: 0.8742 (mmm) REVERT: B 528 MET cc_start: 0.8694 (tpp) cc_final: 0.8241 (tpp) REVERT: B 554 MET cc_start: 0.8483 (tpt) cc_final: 0.8236 (tpt) REVERT: B 568 LEU cc_start: 0.8978 (mp) cc_final: 0.8763 (mp) REVERT: B 577 MET cc_start: 0.8593 (tpp) cc_final: 0.8059 (tpp) REVERT: B 608 LEU cc_start: 0.9369 (mp) cc_final: 0.9012 (tt) REVERT: B 635 ASP cc_start: 0.8642 (t0) cc_final: 0.8374 (t0) REVERT: C 29 TRP cc_start: 0.6735 (t-100) cc_final: 0.6470 (t60) REVERT: C 51 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8390 (mt) REVERT: C 110 MET cc_start: 0.7868 (mtp) cc_final: 0.7098 (mmm) REVERT: C 113 GLU cc_start: 0.9377 (tt0) cc_final: 0.9050 (tp30) REVERT: C 118 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: C 122 HIS cc_start: 0.9243 (m90) cc_final: 0.8402 (m90) REVERT: C 176 GLU cc_start: 0.9267 (mp0) cc_final: 0.9059 (mp0) REVERT: C 178 ILE cc_start: 0.9548 (mp) cc_final: 0.9304 (mm) REVERT: C 242 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9027 (t) REVERT: C 302 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7798 (tpp-160) REVERT: C 318 SER cc_start: 0.9794 (t) cc_final: 0.9525 (p) REVERT: C 383 ASP cc_start: 0.8970 (t0) cc_final: 0.8629 (m-30) REVERT: C 435 MET cc_start: 0.9001 (mmt) cc_final: 0.8052 (mmm) REVERT: C 515 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 528 MET cc_start: 0.8740 (tpp) cc_final: 0.8324 (tpp) REVERT: C 577 MET cc_start: 0.8685 (tpp) cc_final: 0.8229 (tpp) REVERT: C 635 ASP cc_start: 0.8597 (t0) cc_final: 0.8204 (t0) REVERT: D 29 TRP cc_start: 0.6796 (t-100) cc_final: 0.6480 (t60) REVERT: D 66 LYS cc_start: 0.9121 (mttt) cc_final: 0.8867 (mttp) REVERT: D 92 LEU cc_start: 0.9382 (pp) cc_final: 0.9021 (pt) REVERT: D 96 MET cc_start: 0.9330 (ptp) cc_final: 0.8884 (ptp) REVERT: D 99 MET cc_start: 0.8884 (mtp) cc_final: 0.8491 (mtp) REVERT: D 177 GLU cc_start: 0.9232 (pm20) cc_final: 0.8895 (pm20) REVERT: D 178 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.8896 (mm) REVERT: D 215 MET cc_start: 0.9100 (mmt) cc_final: 0.8862 (mmp) REVERT: D 302 ARG cc_start: 0.8183 (tpm170) cc_final: 0.7711 (tpm170) REVERT: D 318 SER cc_start: 0.9767 (t) cc_final: 0.9511 (p) REVERT: D 331 MET cc_start: 0.8524 (tpp) cc_final: 0.7774 (tmm) REVERT: D 383 ASP cc_start: 0.9003 (t0) cc_final: 0.8508 (m-30) REVERT: D 435 MET cc_start: 0.8864 (mmt) cc_final: 0.7913 (mmt) REVERT: D 466 MET cc_start: 0.9390 (mtt) cc_final: 0.8978 (mmm) REVERT: D 554 MET cc_start: 0.8630 (tpt) cc_final: 0.8274 (tpt) REVERT: D 577 MET cc_start: 0.8427 (tpp) cc_final: 0.7971 (tpp) REVERT: D 587 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8376 (t70) REVERT: D 603 MET cc_start: 0.8794 (ttt) cc_final: 0.8536 (tmm) REVERT: D 635 ASP cc_start: 0.8590 (t0) cc_final: 0.8200 (t0) outliers start: 38 outliers final: 29 residues processed: 375 average time/residue: 0.1142 time to fit residues: 70.9697 Evaluate side-chains 373 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 403 GLU 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 200 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 B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 118 GLN 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 C residue 592 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 499 VAL Chi-restraints excluded: chain D residue 520 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 147 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.100384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078387 restraints weight = 53407.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081616 restraints weight = 26442.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083828 restraints weight = 16363.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085150 restraints weight = 11626.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086334 restraints weight = 9321.319| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20209 Z= 0.124 Angle : 0.779 11.172 27424 Z= 0.372 Chirality : 0.043 0.205 3102 Planarity : 0.004 0.048 3454 Dihedral : 6.813 79.042 2805 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.60 % Allowed : 22.26 % Favored : 76.13 % 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 aren not related in a simple way. whole: -1.49 (0.18), residues: 2436 helix: 0.13 (0.15), residues: 1388 sheet: -2.64 (0.60), residues: 68 loop : -2.55 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 75 TYR 0.022 0.001 TYR C 324 PHE 0.012 0.001 PHE A 211 TRP 0.008 0.001 TRP B 629 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00292 (20209) covalent geometry : angle 0.77870 (27424) hydrogen bonds : bond 0.03045 ( 760) hydrogen bonds : angle 4.21293 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3938.53 seconds wall clock time: 68 minutes 26.11 seconds (4106.11 seconds total)