Starting phenix.real_space_refine on Tue Jun 17 12:41:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4c_22664/06_2025/7k4c_22664_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4c_22664/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4c_22664/06_2025/7k4c_22664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4c_22664/06_2025/7k4c_22664.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4c_22664/06_2025/7k4c_22664_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4c_22664/06_2025/7k4c_22664_neut.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.62, per 1000 atoms: 0.64 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: 5.32 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.17 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: 6.09 Time building geometry restraints manager: 6.38 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 638 or resid 701)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 28 through 638 or resid 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.970 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.070 ------------------------------------------------------------------------------- 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 : 5.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP C 613 HIS 0.012 0.002 HIS A 522 PHE 0.029 0.003 PHE A 468 TYR 0.025 0.003 TYR D 623 ARG 0.006 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.30745 ( 760) hydrogen bonds : angle 8.92258 ( 2220) covalent geometry : bond 0.00926 (20209) covalent geometry : angle 1.08836 (27424) *********************** 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 : 2.184 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: 0.8737 (m-30) REVERT: A 402 VAL cc_start: 0.9265 (p) cc_final: 0.8575 (p) REVERT: A 435 MET cc_start: 0.8824 (mmt) cc_final: 0.8011 (mmm) REVERT: A 440 MET cc_start: 0.8875 (tpt) cc_final: 0.8594 (tpp) REVERT: A 442 MET cc_start: 0.9316 (tpp) cc_final: 0.8623 (tpp) REVERT: A 444 LEU cc_start: 0.9467 (mp) cc_final: 0.9172 (mt) REVERT: A 515 GLU cc_start: 0.7496 (tp30) cc_final: 0.7265 (mm-30) REVERT: A 587 HIS cc_start: 0.8857 (p-80) cc_final: 0.8201 (p-80) REVERT: A 588 GLU cc_start: 0.9061 (tt0) cc_final: 0.8781 (tt0) REVERT: A 590 ASP cc_start: 0.8562 (m-30) cc_final: 0.8077 (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: 0.8710 (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: 0.8597 (p-80) REVERT: B 588 GLU cc_start: 0.9060 (tt0) cc_final: 0.8752 (tt0) REVERT: C 92 LEU cc_start: 0.9621 (pp) cc_final: 0.9060 (pp) REVERT: C 96 MET cc_start: 0.9303 (mmm) cc_final: 0.8721 (mmm) REVERT: C 122 HIS cc_start: 0.9387 (m90) cc_final: 0.8612 (m90) REVERT: C 127 ASN cc_start: 0.9220 (t160) cc_final: 0.8949 (m-40) REVERT: C 178 ILE cc_start: 0.9529 (mp) cc_final: 0.9255 (mp) REVERT: C 260 MET cc_start: 0.8946 (tpp) cc_final: 0.8742 (tpp) REVERT: C 279 ASP cc_start: 0.8888 (t70) cc_final: 0.8536 (t0) REVERT: C 303 GLU cc_start: 0.8771 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 305 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8324 (ttm-80) REVERT: C 323 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8489 (mmt180) REVERT: C 332 LEU cc_start: 0.9330 (tp) cc_final: 0.9030 (tt) REVERT: C 386 LEU cc_start: 0.9343 (tp) cc_final: 0.9117 (mm) REVERT: C 402 VAL cc_start: 0.9246 (p) cc_final: 0.8670 (p) REVERT: C 435 MET cc_start: 0.8890 (mmt) cc_final: 0.8296 (mmt) REVERT: C 440 MET cc_start: 0.8731 (tpt) cc_final: 0.8519 (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: 0.9189 (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: 0.3152 time to fit residues: 282.1775 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 : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 118 GLN A 197 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 197 ASN D 483 GLN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074074 restraints weight = 55666.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077114 restraints weight = 27190.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079212 restraints weight = 16837.972| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20209 Z= 0.228 Angle : 0.803 10.303 27424 Z= 0.414 Chirality : 0.044 0.163 3102 Planarity : 0.005 0.067 3454 Dihedral : 10.068 89.720 2805 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.50 % Allowed : 12.83 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.15), residues: 2436 helix: -1.70 (0.12), residues: 1392 sheet: -3.12 (0.53), residues: 68 loop : -3.15 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.005 0.001 HIS A 258 PHE 0.019 0.002 PHE D 162 TYR 0.029 0.002 TYR C 324 ARG 0.004 0.001 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 760) hydrogen bonds : angle 5.61321 ( 2220) covalent geometry : bond 0.00494 (20209) covalent geometry : angle 0.80252 (27424) *********************** 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 452 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 399 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9443 (pp) cc_final: 0.8912 (pp) REVERT: A 96 MET cc_start: 0.9132 (mmm) cc_final: 0.8582 (mmp) REVERT: A 122 HIS cc_start: 0.9438 (m90) cc_final: 0.8690 (m90) REVERT: A 383 ASP cc_start: 0.9158 (t0) cc_final: 0.8664 (m-30) REVERT: A 435 MET cc_start: 0.8918 (mmt) cc_final: 0.8093 (mmm) REVERT: A 440 MET cc_start: 0.8945 (tpt) cc_final: 0.8682 (tpp) REVERT: A 442 MET cc_start: 0.9036 (tpp) cc_final: 0.8733 (mmm) REVERT: A 444 LEU cc_start: 0.9577 (mp) cc_final: 0.9199 (mt) REVERT: A 466 MET cc_start: 0.9458 (mtt) cc_final: 0.9176 (mmt) REVERT: A 515 GLU cc_start: 0.7500 (tp30) cc_final: 0.6944 (mm-30) REVERT: A 528 MET cc_start: 0.8645 (tpp) cc_final: 0.8358 (tpp) REVERT: A 554 MET cc_start: 0.8584 (tpt) cc_final: 0.8375 (tpt) REVERT: A 577 MET cc_start: 0.8844 (tpp) cc_final: 0.8544 (tpp) REVERT: A 578 MET cc_start: 0.8149 (mmt) cc_final: 0.7931 (mmt) REVERT: A 587 HIS cc_start: 0.8963 (p-80) cc_final: 0.8351 (p-80) REVERT: A 590 ASP cc_start: 0.8694 (m-30) cc_final: 0.8148 (p0) REVERT: A 603 MET cc_start: 0.8756 (ttt) cc_final: 0.8474 (tmm) REVERT: A 635 ASP cc_start: 0.8682 (t0) cc_final: 0.8317 (t0) REVERT: B 92 LEU cc_start: 0.9458 (pp) cc_final: 0.8941 (pp) REVERT: B 122 HIS cc_start: 0.9429 (m90) cc_final: 0.8651 (m90) REVERT: B 159 LEU cc_start: 0.9454 (tp) cc_final: 0.9131 (tt) REVERT: B 383 ASP cc_start: 0.9146 (t0) cc_final: 0.8581 (m-30) REVERT: B 435 MET cc_start: 0.8948 (mmt) cc_final: 0.8128 (mmm) REVERT: B 440 MET cc_start: 0.8925 (tpt) cc_final: 0.8648 (tpp) REVERT: B 442 MET cc_start: 0.9109 (tpp) cc_final: 0.8769 (mmm) REVERT: B 444 LEU cc_start: 0.9577 (mp) cc_final: 0.9211 (mt) REVERT: B 481 MET cc_start: 0.8538 (tpp) cc_final: 0.8213 (tpp) REVERT: B 483 GLN cc_start: 0.8335 (tt0) cc_final: 0.8082 (tm-30) REVERT: B 528 MET cc_start: 0.8675 (tpp) cc_final: 0.8426 (tpp) REVERT: B 554 MET cc_start: 0.8733 (tpt) cc_final: 0.8471 (tpt) REVERT: B 577 MET cc_start: 0.8803 (tpp) cc_final: 0.8602 (tpp) REVERT: B 587 HIS cc_start: 0.8976 (p-80) cc_final: 0.8363 (p-80) REVERT: B 590 ASP cc_start: 0.8712 (m-30) cc_final: 0.8105 (p0) REVERT: C 92 LEU cc_start: 0.9486 (pp) cc_final: 0.8927 (pp) REVERT: C 122 HIS cc_start: 0.9415 (m90) cc_final: 0.8681 (m90) REVERT: C 159 LEU cc_start: 0.9457 (tp) cc_final: 0.9136 (tt) REVERT: C 383 ASP cc_start: 0.9152 (t0) cc_final: 0.8614 (m-30) REVERT: C 435 MET cc_start: 0.8972 (mmt) cc_final: 0.8091 (mmt) REVERT: C 442 MET cc_start: 0.9167 (tpp) cc_final: 0.8552 (tpp) REVERT: C 481 MET cc_start: 0.8510 (tpp) cc_final: 0.8208 (tpp) REVERT: C 515 GLU cc_start: 0.7707 (tp30) cc_final: 0.7413 (mm-30) REVERT: C 587 HIS cc_start: 0.9010 (p-80) cc_final: 0.8413 (p-80) REVERT: C 590 ASP cc_start: 0.8745 (m-30) cc_final: 0.8102 (p0) REVERT: D 66 LYS cc_start: 0.9529 (tppt) cc_final: 0.9074 (tptp) REVERT: D 92 LEU cc_start: 0.9503 (pp) cc_final: 0.8974 (pp) REVERT: D 96 MET cc_start: 0.9078 (mmm) cc_final: 0.8449 (mmp) REVERT: D 137 LEU cc_start: 0.9757 (mp) cc_final: 0.9532 (pp) REVERT: D 159 LEU cc_start: 0.9410 (tp) cc_final: 0.9090 (tt) REVERT: D 178 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.8832 (mm) REVERT: D 318 SER cc_start: 0.9766 (t) cc_final: 0.9485 (p) REVERT: D 383 ASP cc_start: 0.9126 (t0) cc_final: 0.8551 (m-30) REVERT: D 435 MET cc_start: 0.8892 (mmt) cc_final: 0.8069 (mmt) REVERT: D 440 MET cc_start: 0.9126 (tpt) cc_final: 0.8898 (tpp) REVERT: D 442 MET cc_start: 0.9152 (tpp) cc_final: 0.8699 (tmm) REVERT: D 444 LEU cc_start: 0.9576 (mp) cc_final: 0.9228 (mt) REVERT: D 466 MET cc_start: 0.9432 (mtt) cc_final: 0.9023 (mmt) REVERT: D 485 MET cc_start: 0.8153 (ttm) cc_final: 0.7706 (ttm) REVERT: D 554 MET cc_start: 0.8719 (tpt) cc_final: 0.8451 (tpt) REVERT: D 578 MET cc_start: 0.8119 (mmt) cc_final: 0.7782 (mmt) REVERT: D 587 HIS cc_start: 0.8992 (p-80) cc_final: 0.8596 (p-80) REVERT: D 590 ASP cc_start: 0.8717 (m-30) cc_final: 0.8223 (p0) REVERT: D 603 MET cc_start: 0.8793 (ttt) cc_final: 0.8513 (tmm) outliers start: 53 outliers final: 29 residues processed: 429 average time/residue: 0.3142 time to fit residues: 216.6349 Evaluate side-chains 372 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 342 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU 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 259 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 232 LEU 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 499 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU 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 25 optimal weight: 4.9990 chunk 210 optimal weight: 0.0050 chunk 122 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 234 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 464 ASN B 522 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.096972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075022 restraints weight = 54738.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078107 restraints weight = 26644.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080274 restraints weight = 16489.790| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20209 Z= 0.157 Angle : 0.706 11.358 27424 Z= 0.357 Chirality : 0.042 0.179 3102 Planarity : 0.005 0.068 3454 Dihedral : 9.546 89.536 2805 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.82 % Allowed : 13.63 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.16), residues: 2436 helix: -0.91 (0.13), residues: 1400 sheet: -2.95 (0.56), residues: 68 loop : -3.14 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 613 HIS 0.005 0.001 HIS A 258 PHE 0.016 0.001 PHE D 162 TYR 0.022 0.001 TYR C 324 ARG 0.009 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 760) hydrogen bonds : angle 4.96060 ( 2220) covalent geometry : bond 0.00351 (20209) covalent geometry : angle 0.70632 (27424) *********************** 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 464 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 383 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9492 (pp) cc_final: 0.9042 (pp) REVERT: A 96 MET cc_start: 0.9050 (mmm) cc_final: 0.8814 (mmp) REVERT: A 99 MET cc_start: 0.8919 (mtp) cc_final: 0.8654 (ptp) REVERT: A 122 HIS cc_start: 0.9382 (m90) cc_final: 0.8654 (m90) REVERT: A 132 LEU cc_start: 0.9235 (mt) cc_final: 0.9025 (mt) REVERT: A 200 LEU cc_start: 0.9342 (mt) cc_final: 0.9131 (mt) REVERT: A 281 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8726 (p) REVERT: A 383 ASP cc_start: 0.9090 (t0) cc_final: 0.8588 (m-30) REVERT: A 440 MET cc_start: 0.9034 (tpt) cc_final: 0.8701 (tmm) REVERT: A 442 MET cc_start: 0.9020 (tpp) cc_final: 0.8706 (mmm) REVERT: A 444 LEU cc_start: 0.9553 (mp) cc_final: 0.9316 (mt) REVERT: A 466 MET cc_start: 0.9455 (mtt) cc_final: 0.9196 (mmt) REVERT: A 515 GLU cc_start: 0.7347 (tp30) cc_final: 0.6823 (mm-30) REVERT: A 528 MET cc_start: 0.8536 (tpp) cc_final: 0.8312 (tpp) REVERT: A 554 MET cc_start: 0.8597 (tpt) cc_final: 0.8295 (tpt) REVERT: A 577 MET cc_start: 0.8823 (tpp) cc_final: 0.8613 (tpp) REVERT: A 587 HIS cc_start: 0.8897 (p-80) cc_final: 0.8346 (p-80) REVERT: A 590 ASP cc_start: 0.8703 (m-30) cc_final: 0.8135 (p0) REVERT: A 603 MET cc_start: 0.8791 (ttt) cc_final: 0.8479 (tmm) REVERT: A 635 ASP cc_start: 0.8583 (t0) cc_final: 0.8196 (t0) REVERT: B 122 HIS cc_start: 0.9372 (m90) cc_final: 0.8605 (m90) REVERT: B 159 LEU cc_start: 0.9431 (tp) cc_final: 0.9101 (tt) REVERT: B 281 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 345 MET cc_start: 0.8898 (tpp) cc_final: 0.8529 (tpp) REVERT: B 383 ASP cc_start: 0.9073 (t0) cc_final: 0.8605 (m-30) REVERT: B 435 MET cc_start: 0.8884 (mmt) cc_final: 0.7977 (mmm) REVERT: B 440 MET cc_start: 0.9071 (tpt) cc_final: 0.8782 (tpp) REVERT: B 442 MET cc_start: 0.9075 (tpp) cc_final: 0.8759 (mmm) REVERT: B 444 LEU cc_start: 0.9552 (mp) cc_final: 0.9208 (mt) REVERT: B 481 MET cc_start: 0.8514 (tpp) cc_final: 0.8210 (tpp) REVERT: B 483 GLN cc_start: 0.8279 (tt0) cc_final: 0.8079 (tm-30) REVERT: B 515 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 554 MET cc_start: 0.8670 (tpt) cc_final: 0.8292 (tpt) REVERT: B 577 MET cc_start: 0.8844 (tpp) cc_final: 0.8534 (tpp) REVERT: B 587 HIS cc_start: 0.8925 (p-80) cc_final: 0.8293 (p-80) REVERT: B 590 ASP cc_start: 0.8760 (m-30) cc_final: 0.8101 (p0) REVERT: B 603 MET cc_start: 0.8526 (ppp) cc_final: 0.8278 (ppp) REVERT: B 635 ASP cc_start: 0.8588 (t0) cc_final: 0.8152 (t0) REVERT: C 122 HIS cc_start: 0.9368 (m90) cc_final: 0.8601 (m90) REVERT: C 159 LEU cc_start: 0.9443 (tp) cc_final: 0.9131 (tt) REVERT: C 318 SER cc_start: 0.9783 (t) cc_final: 0.9529 (p) REVERT: C 383 ASP cc_start: 0.9092 (t0) cc_final: 0.8629 (m-30) REVERT: C 435 MET cc_start: 0.9010 (mmt) cc_final: 0.8156 (mmm) REVERT: C 442 MET cc_start: 0.9195 (tpp) cc_final: 0.8835 (mmm) REVERT: C 481 MET cc_start: 0.8495 (tpp) cc_final: 0.8245 (tpp) REVERT: C 515 GLU cc_start: 0.7633 (tp30) cc_final: 0.7279 (mm-30) REVERT: C 578 MET cc_start: 0.8134 (mmt) cc_final: 0.7722 (mmt) REVERT: C 587 HIS cc_start: 0.8929 (p-80) cc_final: 0.8260 (p-80) REVERT: C 590 ASP cc_start: 0.8793 (m-30) cc_final: 0.8116 (p0) REVERT: C 635 ASP cc_start: 0.8625 (t0) cc_final: 0.7990 (t0) REVERT: D 66 LYS cc_start: 0.9528 (tppt) cc_final: 0.9051 (tptp) REVERT: D 122 HIS cc_start: 0.9464 (m90) cc_final: 0.8864 (m90) REVERT: D 178 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8932 (mm) REVERT: D 290 GLN cc_start: 0.8541 (pp30) cc_final: 0.8264 (pp30) REVERT: D 318 SER cc_start: 0.9763 (t) cc_final: 0.9488 (p) REVERT: D 331 MET cc_start: 0.8554 (tpp) cc_final: 0.7815 (tmm) REVERT: D 345 MET cc_start: 0.9042 (tpp) cc_final: 0.8783 (tpp) REVERT: D 383 ASP cc_start: 0.9045 (t0) cc_final: 0.8478 (m-30) REVERT: D 435 MET cc_start: 0.8883 (mmt) cc_final: 0.8079 (mmt) REVERT: D 440 MET cc_start: 0.9177 (tpt) cc_final: 0.8905 (tpp) REVERT: D 442 MET cc_start: 0.9141 (tpp) cc_final: 0.8816 (mmm) REVERT: D 444 LEU cc_start: 0.9580 (mp) cc_final: 0.9244 (mt) REVERT: D 466 MET cc_start: 0.9397 (mtt) cc_final: 0.9058 (mmt) REVERT: D 485 MET cc_start: 0.8306 (ttm) cc_final: 0.7627 (ttm) REVERT: D 528 MET cc_start: 0.8819 (tpp) cc_final: 0.8541 (tpp) REVERT: D 554 MET cc_start: 0.8616 (tpt) cc_final: 0.8265 (tpt) REVERT: D 577 MET cc_start: 0.8689 (tpp) cc_final: 0.8352 (tpp) REVERT: D 578 MET cc_start: 0.8060 (mmt) cc_final: 0.7704 (mmt) REVERT: D 587 HIS cc_start: 0.8944 (p-80) cc_final: 0.8458 (p-80) REVERT: D 590 ASP cc_start: 0.8707 (m-30) cc_final: 0.8200 (p0) REVERT: D 603 MET cc_start: 0.8760 (ttt) cc_final: 0.8437 (tmm) REVERT: D 635 ASP cc_start: 0.8542 (t0) cc_final: 0.8176 (t0) outliers start: 81 outliers final: 41 residues processed: 442 average time/residue: 0.3946 time to fit residues: 281.7383 Evaluate side-chains 389 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 345 time to evaluate : 2.679 ------------------------------------------------------------------------------- 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 281 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 480 ILE 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 A residue 604 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 91 ASN 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 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 455 SER 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 600 THR 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 26 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072873 restraints weight = 55657.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075923 restraints weight = 27163.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078066 restraints weight = 16807.539| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20209 Z= 0.209 Angle : 0.741 10.993 27424 Z= 0.372 Chirality : 0.044 0.162 3102 Planarity : 0.005 0.060 3454 Dihedral : 9.496 89.059 2805 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.44 % Allowed : 15.19 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.17), residues: 2436 helix: -0.62 (0.13), residues: 1416 sheet: -2.90 (0.57), residues: 68 loop : -3.10 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 613 HIS 0.005 0.001 HIS C 258 PHE 0.021 0.001 PHE D 162 TYR 0.022 0.002 TYR A 324 ARG 0.004 0.000 ARG D 470 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 760) hydrogen bonds : angle 4.92161 ( 2220) covalent geometry : bond 0.00463 (20209) covalent geometry : angle 0.74112 (27424) *********************** 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 423 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 350 time to evaluate : 4.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9496 (pp) cc_final: 0.9091 (pp) REVERT: A 99 MET cc_start: 0.8790 (mtp) cc_final: 0.8472 (ptp) REVERT: A 122 HIS cc_start: 0.9380 (m90) cc_final: 0.8732 (m90) REVERT: A 331 MET cc_start: 0.8535 (tpp) cc_final: 0.7692 (tmm) REVERT: A 383 ASP cc_start: 0.9093 (t0) cc_final: 0.8604 (m-30) REVERT: A 435 MET cc_start: 0.8934 (mmt) cc_final: 0.8030 (mmm) REVERT: A 440 MET cc_start: 0.9086 (tpt) cc_final: 0.8775 (tmm) REVERT: A 444 LEU cc_start: 0.9534 (mp) cc_final: 0.9305 (mt) REVERT: A 466 MET cc_start: 0.9510 (mtt) cc_final: 0.9200 (mmt) REVERT: A 515 GLU cc_start: 0.7531 (tp30) cc_final: 0.6984 (mm-30) REVERT: A 528 MET cc_start: 0.8718 (tpp) cc_final: 0.8476 (tpp) REVERT: A 554 MET cc_start: 0.8548 (tpt) cc_final: 0.8295 (tpt) REVERT: A 577 MET cc_start: 0.8850 (tpp) cc_final: 0.8566 (tpp) REVERT: A 578 MET cc_start: 0.8215 (mmt) cc_final: 0.7815 (mmt) REVERT: A 587 HIS cc_start: 0.8901 (p-80) cc_final: 0.8497 (p-80) REVERT: A 590 ASP cc_start: 0.8639 (m-30) cc_final: 0.7994 (p0) REVERT: A 635 ASP cc_start: 0.8618 (t0) cc_final: 0.8215 (t0) REVERT: B 99 MET cc_start: 0.9158 (mtp) cc_final: 0.8873 (ptp) REVERT: B 122 HIS cc_start: 0.9337 (m90) cc_final: 0.8661 (m90) REVERT: B 159 LEU cc_start: 0.9428 (tp) cc_final: 0.9082 (tt) REVERT: B 331 MET cc_start: 0.8512 (tpp) cc_final: 0.7695 (tmm) REVERT: B 383 ASP cc_start: 0.9118 (t0) cc_final: 0.8610 (m-30) REVERT: B 435 MET cc_start: 0.8931 (mmt) cc_final: 0.8035 (mmm) REVERT: B 440 MET cc_start: 0.9160 (tpt) cc_final: 0.8806 (tmm) REVERT: B 442 MET cc_start: 0.9020 (tpp) cc_final: 0.8687 (mmm) REVERT: B 444 LEU cc_start: 0.9531 (mp) cc_final: 0.9301 (mt) REVERT: B 481 MET cc_start: 0.8415 (tpp) cc_final: 0.8138 (tpp) REVERT: B 485 MET cc_start: 0.8329 (ttm) cc_final: 0.7593 (ttm) REVERT: B 515 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 554 MET cc_start: 0.8581 (tpt) cc_final: 0.8276 (tpt) REVERT: B 577 MET cc_start: 0.8854 (tpp) cc_final: 0.8557 (tpp) REVERT: B 578 MET cc_start: 0.8125 (mmt) cc_final: 0.7764 (mmt) REVERT: B 603 MET cc_start: 0.8586 (ppp) cc_final: 0.8315 (ppp) REVERT: B 635 ASP cc_start: 0.8629 (t0) cc_final: 0.8353 (t0) REVERT: C 122 HIS cc_start: 0.9327 (m90) cc_final: 0.8646 (m90) REVERT: C 159 LEU cc_start: 0.9418 (tp) cc_final: 0.9069 (tt) REVERT: C 178 ILE cc_start: 0.9700 (mp) cc_final: 0.9490 (mp) REVERT: C 302 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7377 (tpm170) REVERT: C 318 SER cc_start: 0.9787 (t) cc_final: 0.9516 (p) REVERT: C 331 MET cc_start: 0.8546 (tpp) cc_final: 0.7740 (tmm) REVERT: C 383 ASP cc_start: 0.9095 (t0) cc_final: 0.8564 (m-30) REVERT: C 435 MET cc_start: 0.8944 (mmt) cc_final: 0.8023 (mmm) REVERT: C 442 MET cc_start: 0.9184 (tpp) cc_final: 0.8804 (mmm) REVERT: C 474 MET cc_start: 0.8674 (tpp) cc_final: 0.8453 (tpp) REVERT: C 481 MET cc_start: 0.8518 (tpp) cc_final: 0.8248 (tpp) REVERT: C 515 GLU cc_start: 0.7753 (tp30) cc_final: 0.7257 (mm-30) REVERT: C 577 MET cc_start: 0.8709 (tpp) cc_final: 0.8452 (tpp) REVERT: C 578 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7716 (mmt) REVERT: C 635 ASP cc_start: 0.8518 (t0) cc_final: 0.8214 (t0) REVERT: D 66 LYS cc_start: 0.9541 (tppt) cc_final: 0.9096 (tptp) REVERT: D 92 LEU cc_start: 0.9531 (pp) cc_final: 0.9153 (pt) REVERT: D 178 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9068 (mm) REVERT: D 318 SER cc_start: 0.9773 (t) cc_final: 0.9497 (p) REVERT: D 331 MET cc_start: 0.8611 (tpp) cc_final: 0.7857 (tmm) REVERT: D 383 ASP cc_start: 0.9055 (t0) cc_final: 0.8471 (m-30) REVERT: D 403 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 435 MET cc_start: 0.8832 (mmt) cc_final: 0.7968 (mmm) REVERT: D 440 MET cc_start: 0.9259 (tpt) cc_final: 0.8995 (tpp) REVERT: D 442 MET cc_start: 0.9071 (tpp) cc_final: 0.8730 (mmm) REVERT: D 444 LEU cc_start: 0.9573 (mp) cc_final: 0.9220 (mt) REVERT: D 466 MET cc_start: 0.9408 (mtt) cc_final: 0.9053 (mmt) REVERT: D 481 MET cc_start: 0.8490 (tpp) cc_final: 0.8277 (tpp) REVERT: D 485 MET cc_start: 0.8242 (ttm) cc_final: 0.7557 (ttm) REVERT: D 554 MET cc_start: 0.8709 (tpt) cc_final: 0.8270 (tpt) REVERT: D 568 LEU cc_start: 0.9129 (tp) cc_final: 0.8926 (tp) REVERT: D 577 MET cc_start: 0.8766 (tpp) cc_final: 0.8503 (tpp) REVERT: D 578 MET cc_start: 0.7980 (mmt) cc_final: 0.7651 (mmt) REVERT: D 603 MET cc_start: 0.8748 (ttt) cc_final: 0.8371 (tmm) REVERT: D 635 ASP cc_start: 0.8583 (t0) cc_final: 0.8302 (t0) outliers start: 73 outliers final: 50 residues processed: 401 average time/residue: 0.3077 time to fit residues: 202.7045 Evaluate side-chains 383 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 2.347 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 480 ILE 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 A residue 604 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 455 SER 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 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN B 483 GLN B 546 ASN C 197 ASN C 201 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN D 290 GLN D 464 ASN D 522 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076535 restraints weight = 54489.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079741 restraints weight = 26236.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081962 restraints weight = 16064.811| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4582 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= 0.115 Angle : 0.690 11.683 27424 Z= 0.338 Chirality : 0.042 0.157 3102 Planarity : 0.004 0.064 3454 Dihedral : 8.637 84.614 2805 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.02 % Allowed : 16.75 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2436 helix: -0.25 (0.14), residues: 1388 sheet: -2.75 (0.59), residues: 68 loop : -3.02 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 613 HIS 0.006 0.001 HIS B 587 PHE 0.016 0.001 PHE D 162 TYR 0.020 0.001 TYR C 324 ARG 0.005 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 760) hydrogen bonds : angle 4.38737 ( 2220) covalent geometry : bond 0.00254 (20209) covalent geometry : angle 0.68956 (27424) *********************** 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 450 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 386 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6974 (t-100) cc_final: 0.6534 (t60) REVERT: A 92 LEU cc_start: 0.9466 (pp) cc_final: 0.9146 (pp) REVERT: A 110 MET cc_start: 0.7377 (mtp) cc_final: 0.7161 (mmm) REVERT: A 122 HIS cc_start: 0.9370 (m90) cc_final: 0.8687 (m90) REVERT: A 125 VAL cc_start: 0.9586 (t) cc_final: 0.9380 (p) REVERT: A 176 GLU cc_start: 0.9360 (pm20) cc_final: 0.8961 (pm20) REVERT: A 331 MET cc_start: 0.8497 (tpp) cc_final: 0.7677 (tmm) REVERT: A 383 ASP cc_start: 0.9065 (t0) cc_final: 0.8625 (m-30) REVERT: A 435 MET cc_start: 0.8828 (mmt) cc_final: 0.7849 (mmm) REVERT: A 440 MET cc_start: 0.9145 (tpt) cc_final: 0.8852 (tmm) REVERT: A 444 LEU cc_start: 0.9528 (mp) cc_final: 0.9313 (mt) REVERT: A 466 MET cc_start: 0.9482 (mtt) cc_final: 0.9198 (mmt) REVERT: A 474 MET cc_start: 0.8771 (tpp) cc_final: 0.8472 (tpp) REVERT: A 515 GLU cc_start: 0.7391 (tp30) cc_final: 0.6894 (mm-30) REVERT: A 528 MET cc_start: 0.8548 (tpp) cc_final: 0.8222 (tpp) REVERT: A 554 MET cc_start: 0.8449 (tpt) cc_final: 0.8194 (tpt) REVERT: A 577 MET cc_start: 0.8721 (tpp) cc_final: 0.8438 (tpp) REVERT: A 635 ASP cc_start: 0.8581 (t0) cc_final: 0.8299 (t0) REVERT: B 122 HIS cc_start: 0.9330 (m90) cc_final: 0.8613 (m90) REVERT: B 125 VAL cc_start: 0.9541 (t) cc_final: 0.9320 (p) REVERT: B 137 LEU cc_start: 0.9738 (mp) cc_final: 0.9483 (pp) REVERT: B 159 LEU cc_start: 0.9367 (tp) cc_final: 0.9051 (tt) REVERT: B 176 GLU cc_start: 0.9390 (pm20) cc_final: 0.9015 (pm20) REVERT: B 318 SER cc_start: 0.9787 (t) cc_final: 0.9539 (p) REVERT: B 331 MET cc_start: 0.8489 (tpp) cc_final: 0.7692 (tmm) REVERT: B 383 ASP cc_start: 0.9104 (t0) cc_final: 0.8584 (m-30) REVERT: B 386 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8762 (mm) REVERT: B 435 MET cc_start: 0.8844 (mmt) cc_final: 0.7812 (mmm) REVERT: B 440 MET cc_start: 0.9151 (tpt) cc_final: 0.8840 (tmm) REVERT: B 515 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 528 MET cc_start: 0.8498 (tpp) cc_final: 0.8296 (tpp) REVERT: B 554 MET cc_start: 0.8457 (tpt) cc_final: 0.8140 (tpt) REVERT: B 577 MET cc_start: 0.8671 (tpp) cc_final: 0.8354 (tpp) REVERT: B 603 MET cc_start: 0.8623 (ppp) cc_final: 0.8343 (ppp) REVERT: B 635 ASP cc_start: 0.8591 (t0) cc_final: 0.8298 (t0) REVERT: C 122 HIS cc_start: 0.9352 (m90) cc_final: 0.8648 (m90) REVERT: C 159 LEU cc_start: 0.9367 (tp) cc_final: 0.9067 (tt) REVERT: C 176 GLU cc_start: 0.9462 (pm20) cc_final: 0.9170 (mp0) REVERT: C 177 GLU cc_start: 0.9371 (pm20) cc_final: 0.9155 (pm20) REVERT: C 178 ILE cc_start: 0.9587 (mp) cc_final: 0.9305 (mm) REVERT: C 215 MET cc_start: 0.9065 (mmt) cc_final: 0.8733 (mmp) REVERT: C 318 SER cc_start: 0.9769 (t) cc_final: 0.9510 (p) REVERT: C 331 MET cc_start: 0.8532 (tpp) cc_final: 0.7698 (tmm) REVERT: C 383 ASP cc_start: 0.9087 (t0) cc_final: 0.8593 (m-30) REVERT: C 386 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8875 (mm) REVERT: C 435 MET cc_start: 0.8849 (mmt) cc_final: 0.7948 (mmm) REVERT: C 442 MET cc_start: 0.9115 (tpp) cc_final: 0.8728 (mmm) REVERT: C 474 MET cc_start: 0.8746 (tpp) cc_final: 0.8461 (tpp) REVERT: C 515 GLU cc_start: 0.7599 (tp30) cc_final: 0.7181 (mm-30) REVERT: C 528 MET cc_start: 0.8578 (tpp) cc_final: 0.8360 (tpp) REVERT: C 577 MET cc_start: 0.8627 (tpp) cc_final: 0.8314 (tpp) REVERT: C 635 ASP cc_start: 0.8477 (t0) cc_final: 0.8170 (t0) REVERT: D 29 TRP cc_start: 0.6950 (t-100) cc_final: 0.6497 (t60) REVERT: D 177 GLU cc_start: 0.9027 (pm20) cc_final: 0.8734 (pp20) REVERT: D 178 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8940 (mp) REVERT: D 318 SER cc_start: 0.9751 (t) cc_final: 0.9479 (p) REVERT: D 331 MET cc_start: 0.8546 (tpp) cc_final: 0.7786 (tmm) REVERT: D 383 ASP cc_start: 0.8987 (t0) cc_final: 0.8447 (m-30) REVERT: D 435 MET cc_start: 0.8734 (mmt) cc_final: 0.7873 (mmm) REVERT: D 440 MET cc_start: 0.9241 (tpt) cc_final: 0.8937 (tmm) REVERT: D 442 MET cc_start: 0.8960 (tpp) cc_final: 0.8740 (mmm) REVERT: D 466 MET cc_start: 0.9369 (mtt) cc_final: 0.9038 (mmt) REVERT: D 528 MET cc_start: 0.8575 (tpp) cc_final: 0.8345 (tpp) REVERT: D 554 MET cc_start: 0.8392 (tpt) cc_final: 0.8069 (tpt) REVERT: D 603 MET cc_start: 0.8763 (ttt) cc_final: 0.8489 (ppp) REVERT: D 635 ASP cc_start: 0.8526 (t0) cc_final: 0.8244 (t0) outliers start: 64 outliers final: 33 residues processed: 428 average time/residue: 0.2910 time to fit residues: 202.1349 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 : 2.357 ------------------------------------------------------------------------------- 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 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 592 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 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 600 THR 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 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 386 LEU 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 568 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 499 VAL Chi-restraints excluded: chain D residue 520 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 86 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077012 restraints weight = 54103.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080136 restraints weight = 26261.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082350 restraints weight = 16284.809| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20209 Z= 0.118 Angle : 0.701 12.053 27424 Z= 0.341 Chirality : 0.042 0.169 3102 Planarity : 0.004 0.060 3454 Dihedral : 8.285 84.034 2805 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.97 % Allowed : 18.44 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2436 helix: -0.26 (0.14), residues: 1408 sheet: -2.76 (0.59), residues: 68 loop : -3.01 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 613 HIS 0.006 0.001 HIS A 587 PHE 0.027 0.001 PHE C 162 TYR 0.022 0.001 TYR C 324 ARG 0.004 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 760) hydrogen bonds : angle 4.33052 ( 2220) covalent geometry : bond 0.00272 (20209) covalent geometry : angle 0.70109 (27424) *********************** 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 409 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6947 (t-100) cc_final: 0.6525 (t60) REVERT: A 122 HIS cc_start: 0.9348 (m90) cc_final: 0.8647 (m90) REVERT: A 125 VAL cc_start: 0.9581 (t) cc_final: 0.9362 (p) REVERT: A 130 MET cc_start: 0.8687 (ptt) cc_final: 0.8350 (ptt) REVERT: A 176 GLU cc_start: 0.9369 (pm20) cc_final: 0.9096 (pm20) REVERT: A 283 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7538 (mp) REVERT: A 302 ARG cc_start: 0.7984 (tpm170) cc_final: 0.7506 (tpm170) REVERT: A 331 MET cc_start: 0.8481 (tpp) cc_final: 0.7652 (tmm) REVERT: A 383 ASP cc_start: 0.9132 (t0) cc_final: 0.8563 (m-30) REVERT: A 385 ARG cc_start: 0.8375 (ttp-170) cc_final: 0.8159 (ttp80) REVERT: A 435 MET cc_start: 0.8831 (mmt) cc_final: 0.7907 (mmm) REVERT: A 440 MET cc_start: 0.9107 (tpt) cc_final: 0.8839 (tmm) REVERT: A 444 LEU cc_start: 0.9530 (mp) cc_final: 0.9321 (mt) REVERT: A 466 MET cc_start: 0.9474 (mtt) cc_final: 0.9178 (mmt) REVERT: A 474 MET cc_start: 0.8839 (tpp) cc_final: 0.8638 (tpp) REVERT: A 515 GLU cc_start: 0.7429 (tp30) cc_final: 0.7017 (mm-30) REVERT: A 528 MET cc_start: 0.8522 (tpp) cc_final: 0.8204 (tpp) REVERT: A 554 MET cc_start: 0.8430 (tpt) cc_final: 0.8195 (tpt) REVERT: A 577 MET cc_start: 0.8609 (tpp) cc_final: 0.8283 (tpp) REVERT: A 635 ASP cc_start: 0.8594 (t0) cc_final: 0.8344 (t0) REVERT: B 29 TRP cc_start: 0.6935 (t-100) cc_final: 0.6508 (t60) REVERT: B 99 MET cc_start: 0.9189 (ptp) cc_final: 0.8655 (ptp) REVERT: B 122 HIS cc_start: 0.9341 (m90) cc_final: 0.8684 (m90) REVERT: B 125 VAL cc_start: 0.9549 (t) cc_final: 0.9340 (p) REVERT: B 137 LEU cc_start: 0.9716 (mp) cc_final: 0.9446 (pp) REVERT: B 318 SER cc_start: 0.9782 (t) cc_final: 0.9527 (p) REVERT: B 331 MET cc_start: 0.8510 (tpp) cc_final: 0.7682 (tmm) REVERT: B 383 ASP cc_start: 0.9106 (t0) cc_final: 0.8611 (m-30) REVERT: B 435 MET cc_start: 0.8844 (mmt) cc_final: 0.7927 (mmm) REVERT: B 440 MET cc_start: 0.9165 (tpt) cc_final: 0.8919 (tmm) REVERT: B 515 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 528 MET cc_start: 0.8482 (tpp) cc_final: 0.8184 (tpp) REVERT: B 554 MET cc_start: 0.8458 (tpt) cc_final: 0.8150 (tpt) REVERT: B 577 MET cc_start: 0.8553 (tpp) cc_final: 0.8311 (tpp) REVERT: B 603 MET cc_start: 0.8625 (ppp) cc_final: 0.8340 (ppp) REVERT: B 635 ASP cc_start: 0.8609 (t0) cc_final: 0.8343 (t0) REVERT: C 99 MET cc_start: 0.9253 (ptp) cc_final: 0.8703 (ptp) REVERT: C 122 HIS cc_start: 0.9289 (m90) cc_final: 0.8586 (m90) REVERT: C 173 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 176 GLU cc_start: 0.9468 (pm20) cc_final: 0.9187 (mp0) REVERT: C 215 MET cc_start: 0.9018 (mmt) cc_final: 0.8692 (mmp) REVERT: C 242 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8972 (t) REVERT: C 318 SER cc_start: 0.9769 (t) cc_final: 0.9498 (p) REVERT: C 331 MET cc_start: 0.8478 (tpp) cc_final: 0.7660 (tmm) REVERT: C 383 ASP cc_start: 0.9101 (t0) cc_final: 0.8614 (m-30) REVERT: C 435 MET cc_start: 0.8869 (mmt) cc_final: 0.7851 (mmt) REVERT: C 442 MET cc_start: 0.9091 (tpp) cc_final: 0.8717 (mmm) REVERT: C 515 GLU cc_start: 0.7608 (tp30) cc_final: 0.7086 (mm-30) REVERT: C 528 MET cc_start: 0.8481 (tpp) cc_final: 0.8171 (tpp) REVERT: C 577 MET cc_start: 0.8560 (tpp) cc_final: 0.8306 (tpp) REVERT: C 635 ASP cc_start: 0.8488 (t0) cc_final: 0.8180 (t0) REVERT: D 29 TRP cc_start: 0.6944 (t-100) cc_final: 0.6503 (t60) REVERT: D 66 LYS cc_start: 0.9549 (tppt) cc_final: 0.9097 (tptp) REVERT: D 96 MET cc_start: 0.9398 (ptp) cc_final: 0.8978 (ptp) REVERT: D 110 MET cc_start: 0.7387 (mtp) cc_final: 0.6630 (mmt) REVERT: D 130 MET cc_start: 0.8639 (ptt) cc_final: 0.8149 (ptt) REVERT: D 177 GLU cc_start: 0.9079 (pm20) cc_final: 0.8790 (pm20) REVERT: D 178 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8636 (mm) REVERT: D 283 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7399 (mp) REVERT: D 318 SER cc_start: 0.9754 (t) cc_final: 0.9483 (p) REVERT: D 331 MET cc_start: 0.8513 (tpp) cc_final: 0.7784 (tmm) REVERT: D 383 ASP cc_start: 0.8976 (t0) cc_final: 0.8436 (m-30) REVERT: D 435 MET cc_start: 0.8725 (mmt) cc_final: 0.7772 (mmt) REVERT: D 440 MET cc_start: 0.9277 (tpt) cc_final: 0.9054 (tmm) REVERT: D 442 MET cc_start: 0.8945 (tpp) cc_final: 0.8743 (mmm) REVERT: D 466 MET cc_start: 0.9396 (mtt) cc_final: 0.9060 (mmm) REVERT: D 528 MET cc_start: 0.8578 (tpp) cc_final: 0.8277 (tpp) REVERT: D 554 MET cc_start: 0.8422 (tpt) cc_final: 0.8103 (tpt) REVERT: D 603 MET cc_start: 0.8756 (ttt) cc_final: 0.8477 (ppp) REVERT: D 635 ASP cc_start: 0.8526 (t0) cc_final: 0.8239 (t0) outliers start: 63 outliers final: 47 residues processed: 379 average time/residue: 0.3436 time to fit residues: 214.0066 Evaluate side-chains 383 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 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 568 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS 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 177 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 158 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073216 restraints weight = 54757.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076277 restraints weight = 27000.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078383 restraints weight = 16734.751| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20209 Z= 0.203 Angle : 0.757 11.320 27424 Z= 0.373 Chirality : 0.044 0.174 3102 Planarity : 0.004 0.049 3454 Dihedral : 8.627 89.178 2805 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.49 % Allowed : 19.15 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2436 helix: -0.21 (0.14), residues: 1412 sheet: -2.81 (0.60), residues: 68 loop : -2.90 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.006 0.001 HIS A 587 PHE 0.016 0.001 PHE C 162 TYR 0.020 0.002 TYR C 324 ARG 0.006 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 760) hydrogen bonds : angle 4.67127 ( 2220) covalent geometry : bond 0.00454 (20209) covalent geometry : angle 0.75716 (27424) *********************** 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 404 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7583 (mtp) cc_final: 0.6697 (mmt) REVERT: A 122 HIS cc_start: 0.9325 (m90) cc_final: 0.8890 (m-70) REVERT: A 130 MET cc_start: 0.8807 (ptt) cc_final: 0.8385 (ptt) REVERT: A 176 GLU cc_start: 0.9381 (pm20) cc_final: 0.9013 (pm20) REVERT: A 242 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9026 (t) REVERT: A 283 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (mt) REVERT: A 302 ARG cc_start: 0.8030 (tpm170) cc_final: 0.7536 (tpm170) REVERT: A 331 MET cc_start: 0.8520 (tpp) cc_final: 0.7747 (tmm) REVERT: A 383 ASP cc_start: 0.9081 (t0) cc_final: 0.8659 (m-30) REVERT: A 435 MET cc_start: 0.8826 (mmt) cc_final: 0.7857 (mmm) REVERT: A 440 MET cc_start: 0.9177 (tpt) cc_final: 0.8911 (tmm) REVERT: A 444 LEU cc_start: 0.9541 (mp) cc_final: 0.9337 (mt) REVERT: A 454 MET cc_start: 0.9012 (tpt) cc_final: 0.8785 (tpt) REVERT: A 466 MET cc_start: 0.9508 (mtt) cc_final: 0.9205 (mmt) REVERT: A 515 GLU cc_start: 0.7601 (tp30) cc_final: 0.7395 (mm-30) REVERT: A 528 MET cc_start: 0.8787 (tpp) cc_final: 0.8468 (tpp) REVERT: A 554 MET cc_start: 0.8562 (tpt) cc_final: 0.8305 (tpt) REVERT: A 577 MET cc_start: 0.8730 (tpp) cc_final: 0.8480 (tpp) REVERT: A 635 ASP cc_start: 0.8583 (t0) cc_final: 0.8206 (t0) REVERT: B 159 LEU cc_start: 0.9393 (tp) cc_final: 0.9063 (tt) REVERT: B 176 GLU cc_start: 0.9431 (pm20) cc_final: 0.8990 (pm20) REVERT: B 242 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9069 (t) REVERT: B 283 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 331 MET cc_start: 0.8511 (tpp) cc_final: 0.7727 (tmm) REVERT: B 383 ASP cc_start: 0.9142 (t0) cc_final: 0.8612 (m-30) REVERT: B 435 MET cc_start: 0.8833 (mmt) cc_final: 0.7870 (mmm) REVERT: B 440 MET cc_start: 0.9190 (tpt) cc_final: 0.8957 (tmm) REVERT: B 554 MET cc_start: 0.8508 (tpt) cc_final: 0.8176 (tpt) REVERT: B 577 MET cc_start: 0.8775 (tpp) cc_final: 0.8477 (tpp) REVERT: B 603 MET cc_start: 0.8674 (ppp) cc_final: 0.8388 (ppp) REVERT: B 635 ASP cc_start: 0.8647 (t0) cc_final: 0.8240 (t0) REVERT: C 122 HIS cc_start: 0.9279 (m90) cc_final: 0.8865 (m-70) REVERT: C 176 GLU cc_start: 0.9443 (pm20) cc_final: 0.9050 (mp0) REVERT: C 177 GLU cc_start: 0.9275 (pm20) cc_final: 0.8986 (pm20) REVERT: C 215 MET cc_start: 0.8948 (mmt) cc_final: 0.8674 (mmp) REVERT: C 318 SER cc_start: 0.9788 (t) cc_final: 0.9512 (p) REVERT: C 331 MET cc_start: 0.8554 (tpp) cc_final: 0.7736 (tmm) REVERT: C 383 ASP cc_start: 0.9134 (t0) cc_final: 0.8620 (m-30) REVERT: C 435 MET cc_start: 0.8896 (mmt) cc_final: 0.7898 (mmm) REVERT: C 442 MET cc_start: 0.9112 (tpp) cc_final: 0.8724 (mmm) REVERT: C 515 GLU cc_start: 0.7787 (tp30) cc_final: 0.7218 (mm-30) REVERT: C 577 MET cc_start: 0.8727 (tpp) cc_final: 0.8402 (tpp) REVERT: C 635 ASP cc_start: 0.8540 (t0) cc_final: 0.8153 (t0) REVERT: D 66 LYS cc_start: 0.9561 (tppt) cc_final: 0.9124 (tptp) REVERT: D 130 MET cc_start: 0.8730 (ptt) cc_final: 0.8175 (ptt) REVERT: D 177 GLU cc_start: 0.9189 (pm20) cc_final: 0.8918 (pm20) REVERT: D 178 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.8992 (mm) REVERT: D 215 MET cc_start: 0.9320 (mmt) cc_final: 0.9065 (mmp) REVERT: D 318 SER cc_start: 0.9764 (t) cc_final: 0.9490 (p) REVERT: D 331 MET cc_start: 0.8587 (tpp) cc_final: 0.7837 (tmm) REVERT: D 383 ASP cc_start: 0.9015 (t0) cc_final: 0.8465 (m-30) REVERT: D 435 MET cc_start: 0.8807 (mmt) cc_final: 0.7870 (mmt) REVERT: D 440 MET cc_start: 0.9296 (tpt) cc_final: 0.9063 (tmm) REVERT: D 442 MET cc_start: 0.8992 (tpp) cc_final: 0.8691 (mmm) REVERT: D 445 ILE cc_start: 0.9568 (tp) cc_final: 0.9243 (pt) REVERT: D 466 MET cc_start: 0.9477 (mtt) cc_final: 0.9101 (mmm) REVERT: D 554 MET cc_start: 0.8524 (tpt) cc_final: 0.8206 (tpt) REVERT: D 603 MET cc_start: 0.8743 (ttt) cc_final: 0.8508 (ppp) REVERT: D 635 ASP cc_start: 0.8544 (t0) cc_final: 0.8194 (t0) outliers start: 74 outliers final: 52 residues processed: 376 average time/residue: 0.2768 time to fit residues: 170.3863 Evaluate side-chains 380 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 323 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 125 VAL 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 311 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 57 ASP 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 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 173 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.095421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073730 restraints weight = 54654.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076855 restraints weight = 26785.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079003 restraints weight = 16514.473| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20209 Z= 0.161 Angle : 0.753 13.742 27424 Z= 0.366 Chirality : 0.044 0.203 3102 Planarity : 0.004 0.051 3454 Dihedral : 8.416 87.744 2805 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.21 % Allowed : 19.53 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2436 helix: 0.04 (0.14), residues: 1372 sheet: -2.80 (0.60), residues: 68 loop : -2.74 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.005 0.001 HIS A 587 PHE 0.012 0.001 PHE B 211 TYR 0.019 0.001 TYR C 324 ARG 0.004 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 760) hydrogen bonds : angle 4.50412 ( 2220) covalent geometry : bond 0.00369 (20209) covalent geometry : angle 0.75333 (27424) *********************** 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 406 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 338 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9201 (ppp) cc_final: 0.8828 (pmm) REVERT: A 99 MET cc_start: 0.9049 (ptm) cc_final: 0.8216 (ptp) REVERT: A 110 MET cc_start: 0.7565 (mtp) cc_final: 0.6782 (mmt) REVERT: A 122 HIS cc_start: 0.9329 (m90) cc_final: 0.8854 (m-70) REVERT: A 125 VAL cc_start: 0.9668 (t) cc_final: 0.9445 (p) REVERT: A 130 MET cc_start: 0.8752 (ptt) cc_final: 0.8322 (ptt) REVERT: A 242 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9013 (t) REVERT: A 302 ARG cc_start: 0.8038 (tpm170) cc_final: 0.7580 (tpm170) REVERT: A 331 MET cc_start: 0.8550 (tpp) cc_final: 0.7746 (tmm) REVERT: A 383 ASP cc_start: 0.9118 (t0) cc_final: 0.8586 (m-30) REVERT: A 435 MET cc_start: 0.8800 (mmt) cc_final: 0.7839 (mmt) REVERT: A 440 MET cc_start: 0.9103 (tpt) cc_final: 0.8848 (tmm) REVERT: A 444 LEU cc_start: 0.9561 (mp) cc_final: 0.9361 (mt) REVERT: A 466 MET cc_start: 0.9495 (mtt) cc_final: 0.9205 (mmt) REVERT: A 515 GLU cc_start: 0.7544 (tp30) cc_final: 0.7101 (mm-30) REVERT: A 528 MET cc_start: 0.8682 (tpp) cc_final: 0.8319 (tpp) REVERT: A 554 MET cc_start: 0.8477 (tpt) cc_final: 0.8200 (tpt) REVERT: A 577 MET cc_start: 0.8776 (tpp) cc_final: 0.8525 (tpp) REVERT: A 635 ASP cc_start: 0.8533 (t0) cc_final: 0.8089 (t0) REVERT: B 159 LEU cc_start: 0.9358 (tp) cc_final: 0.9020 (tt) REVERT: B 176 GLU cc_start: 0.9367 (pm20) cc_final: 0.9061 (pm20) REVERT: B 242 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9046 (t) REVERT: B 283 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 318 SER cc_start: 0.9788 (t) cc_final: 0.9526 (p) REVERT: B 331 MET cc_start: 0.8534 (tpp) cc_final: 0.7748 (tmm) REVERT: B 383 ASP cc_start: 0.9121 (t0) cc_final: 0.8586 (m-30) REVERT: B 435 MET cc_start: 0.8813 (mmt) cc_final: 0.7865 (mmm) REVERT: B 554 MET cc_start: 0.8470 (tpt) cc_final: 0.8167 (tpt) REVERT: B 577 MET cc_start: 0.8774 (tpp) cc_final: 0.8483 (tpp) REVERT: B 603 MET cc_start: 0.8711 (ppp) cc_final: 0.8462 (ppp) REVERT: B 635 ASP cc_start: 0.8634 (t0) cc_final: 0.8279 (t0) REVERT: C 122 HIS cc_start: 0.9295 (m90) cc_final: 0.8876 (m-70) REVERT: C 173 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8362 (p) REVERT: C 176 GLU cc_start: 0.9432 (pm20) cc_final: 0.9220 (mp0) REVERT: C 177 GLU cc_start: 0.9331 (pm20) cc_final: 0.9041 (pm20) REVERT: C 215 MET cc_start: 0.8971 (mmt) cc_final: 0.8741 (mmp) REVERT: C 331 MET cc_start: 0.8529 (tpp) cc_final: 0.7728 (tmm) REVERT: C 345 MET cc_start: 0.8800 (tpp) cc_final: 0.8599 (tpp) REVERT: C 383 ASP cc_start: 0.9116 (t0) cc_final: 0.8584 (m-30) REVERT: C 435 MET cc_start: 0.8861 (mmt) cc_final: 0.7844 (mmm) REVERT: C 442 MET cc_start: 0.9130 (tpp) cc_final: 0.8730 (mmm) REVERT: C 515 GLU cc_start: 0.7723 (tp30) cc_final: 0.7146 (mm-30) REVERT: C 577 MET cc_start: 0.8708 (tpp) cc_final: 0.8388 (tpp) REVERT: C 635 ASP cc_start: 0.8544 (t0) cc_final: 0.8179 (t0) REVERT: D 66 LYS cc_start: 0.9561 (tppt) cc_final: 0.9123 (tptp) REVERT: D 110 MET cc_start: 0.7442 (mtp) cc_final: 0.6654 (mmt) REVERT: D 130 MET cc_start: 0.8756 (ptt) cc_final: 0.8211 (ptt) REVERT: D 177 GLU cc_start: 0.9249 (pm20) cc_final: 0.8984 (pm20) REVERT: D 178 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9021 (mm) REVERT: D 215 MET cc_start: 0.9311 (mmt) cc_final: 0.9106 (mmp) REVERT: D 260 MET cc_start: 0.8871 (mmm) cc_final: 0.8596 (tpp) REVERT: D 315 GLU cc_start: 0.9221 (tp30) cc_final: 0.8799 (tp30) REVERT: D 318 SER cc_start: 0.9758 (t) cc_final: 0.9472 (p) REVERT: D 331 MET cc_start: 0.8564 (tpp) cc_final: 0.7805 (tmm) REVERT: D 383 ASP cc_start: 0.8967 (t0) cc_final: 0.8429 (m-30) REVERT: D 435 MET cc_start: 0.8767 (mmt) cc_final: 0.7804 (mmt) REVERT: D 440 MET cc_start: 0.9300 (tpt) cc_final: 0.9087 (tmm) REVERT: D 466 MET cc_start: 0.9518 (mtt) cc_final: 0.9056 (mmm) REVERT: D 554 MET cc_start: 0.8474 (tpt) cc_final: 0.8154 (tpt) REVERT: D 577 MET cc_start: 0.8626 (tpp) cc_final: 0.8361 (tpp) REVERT: D 603 MET cc_start: 0.8735 (ttt) cc_final: 0.8359 (tmm) REVERT: D 635 ASP cc_start: 0.8542 (t0) cc_final: 0.8197 (t0) outliers start: 68 outliers final: 56 residues processed: 380 average time/residue: 0.2735 time to fit residues: 168.6657 Evaluate side-chains 383 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 57 ASP 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 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.0070 chunk 82 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 128 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077376 restraints weight = 54233.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080699 restraints weight = 25798.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082983 restraints weight = 15646.794| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5477 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= 0.118 Angle : 0.748 13.859 27424 Z= 0.357 Chirality : 0.043 0.235 3102 Planarity : 0.004 0.054 3454 Dihedral : 7.527 80.502 2805 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.12 % Allowed : 20.85 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.18), residues: 2436 helix: 0.11 (0.15), residues: 1372 sheet: -2.76 (0.60), residues: 68 loop : -2.74 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 629 HIS 0.004 0.001 HIS A 587 PHE 0.011 0.001 PHE C 162 TYR 0.020 0.001 TYR C 324 ARG 0.008 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 760) hydrogen bonds : angle 4.22022 ( 2220) covalent geometry : bond 0.00268 (20209) covalent geometry : angle 0.74773 (27424) *********************** 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: 45 poor density : 362 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6983 (t-100) cc_final: 0.6562 (t60) REVERT: A 110 MET cc_start: 0.7569 (mtp) cc_final: 0.6861 (mmt) REVERT: A 122 HIS cc_start: 0.9280 (m90) cc_final: 0.8597 (m90) REVERT: A 125 VAL cc_start: 0.9628 (t) cc_final: 0.9395 (p) REVERT: A 130 MET cc_start: 0.8545 (ptt) cc_final: 0.8164 (ptt) REVERT: A 242 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8918 (t) REVERT: A 283 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7444 (mt) REVERT: A 302 ARG cc_start: 0.8179 (tpm170) cc_final: 0.7702 (tpm170) REVERT: A 331 MET cc_start: 0.8492 (tpp) cc_final: 0.7656 (tmm) REVERT: A 383 ASP cc_start: 0.9157 (t0) cc_final: 0.8678 (m-30) REVERT: A 435 MET cc_start: 0.8769 (mmt) cc_final: 0.7748 (mmt) REVERT: A 466 MET cc_start: 0.9373 (mtt) cc_final: 0.9128 (mmt) REVERT: A 515 GLU cc_start: 0.7377 (tp30) cc_final: 0.6959 (mm-30) REVERT: A 528 MET cc_start: 0.8625 (tpp) cc_final: 0.8275 (tpp) REVERT: A 554 MET cc_start: 0.8389 (tpt) cc_final: 0.8145 (tpt) REVERT: A 577 MET cc_start: 0.8585 (tpp) cc_final: 0.8324 (tpp) REVERT: A 608 LEU cc_start: 0.9399 (mp) cc_final: 0.9087 (tt) REVERT: A 635 ASP cc_start: 0.8619 (t0) cc_final: 0.8368 (t0) REVERT: B 29 TRP cc_start: 0.7007 (t-100) cc_final: 0.6591 (t60) REVERT: B 113 GLU cc_start: 0.9404 (tt0) cc_final: 0.9104 (tp30) REVERT: B 125 VAL cc_start: 0.9519 (t) cc_final: 0.9288 (p) REVERT: B 139 ARG cc_start: 0.9649 (mpt180) cc_final: 0.9316 (mmt90) REVERT: B 176 GLU cc_start: 0.9377 (pm20) cc_final: 0.8987 (pm20) REVERT: B 242 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8988 (t) REVERT: B 260 MET cc_start: 0.8835 (mmm) cc_final: 0.8594 (tpp) REVERT: B 302 ARG cc_start: 0.8515 (tpm170) cc_final: 0.8231 (tpm170) REVERT: B 318 SER cc_start: 0.9782 (t) cc_final: 0.9517 (p) REVERT: B 331 MET cc_start: 0.8467 (tpp) cc_final: 0.7663 (tmm) REVERT: B 383 ASP cc_start: 0.9108 (t0) cc_final: 0.8581 (m-30) REVERT: B 435 MET cc_start: 0.8829 (mmt) cc_final: 0.7826 (mmm) REVERT: B 554 MET cc_start: 0.8353 (tpt) cc_final: 0.8077 (tpt) REVERT: B 577 MET cc_start: 0.8561 (tpp) cc_final: 0.8258 (tpp) REVERT: B 603 MET cc_start: 0.8747 (ppp) cc_final: 0.8495 (ppp) REVERT: B 608 LEU cc_start: 0.9376 (mp) cc_final: 0.9058 (tt) REVERT: B 635 ASP cc_start: 0.8614 (t0) cc_final: 0.8360 (t0) REVERT: C 29 TRP cc_start: 0.6963 (t-100) cc_final: 0.6611 (t60) REVERT: C 122 HIS cc_start: 0.9249 (m90) cc_final: 0.8584 (m90) REVERT: C 173 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8101 (p) REVERT: C 177 GLU cc_start: 0.9305 (pm20) cc_final: 0.9083 (pm20) REVERT: C 283 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 318 SER cc_start: 0.9781 (t) cc_final: 0.9519 (p) REVERT: C 331 MET cc_start: 0.8532 (tpp) cc_final: 0.7689 (tmm) REVERT: C 383 ASP cc_start: 0.9092 (t0) cc_final: 0.8560 (m-30) REVERT: C 435 MET cc_start: 0.8827 (mmt) cc_final: 0.7820 (mmm) REVERT: C 442 MET cc_start: 0.9081 (tpp) cc_final: 0.8702 (mmm) REVERT: C 515 GLU cc_start: 0.7456 (tp30) cc_final: 0.7017 (mm-30) REVERT: C 577 MET cc_start: 0.8560 (tpp) cc_final: 0.7916 (tpp) REVERT: C 635 ASP cc_start: 0.8496 (t0) cc_final: 0.8214 (t0) REVERT: D 29 TRP cc_start: 0.6981 (t-100) cc_final: 0.6579 (t60) REVERT: D 66 LYS cc_start: 0.9545 (tppt) cc_final: 0.9078 (tptp) REVERT: D 110 MET cc_start: 0.7357 (mtp) cc_final: 0.6781 (mmt) REVERT: D 130 MET cc_start: 0.8554 (ptt) cc_final: 0.8074 (ptt) REVERT: D 177 GLU cc_start: 0.9227 (pm20) cc_final: 0.8922 (pm20) REVERT: D 178 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.8973 (mm) REVERT: D 215 MET cc_start: 0.9255 (mmt) cc_final: 0.8969 (mmp) REVERT: D 315 GLU cc_start: 0.9160 (tp30) cc_final: 0.8744 (tp30) REVERT: D 318 SER cc_start: 0.9752 (t) cc_final: 0.9467 (p) REVERT: D 331 MET cc_start: 0.8476 (tpp) cc_final: 0.7721 (tmm) REVERT: D 383 ASP cc_start: 0.9064 (t0) cc_final: 0.8585 (m-30) REVERT: D 390 LEU cc_start: 0.9477 (mm) cc_final: 0.9233 (mm) REVERT: D 435 MET cc_start: 0.8719 (mmt) cc_final: 0.7757 (mmt) REVERT: D 466 MET cc_start: 0.9491 (mtt) cc_final: 0.8995 (mmm) REVERT: D 554 MET cc_start: 0.8341 (tpt) cc_final: 0.8073 (tpt) REVERT: D 603 MET cc_start: 0.8780 (ttt) cc_final: 0.8543 (ppp) REVERT: D 635 ASP cc_start: 0.8539 (t0) cc_final: 0.8270 (t0) outliers start: 45 outliers final: 30 residues processed: 383 average time/residue: 0.2698 time to fit residues: 168.1189 Evaluate side-chains 377 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 341 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 587 HIS 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 283 ILE Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 200 LEU 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 538 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075567 restraints weight = 54393.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078712 restraints weight = 26591.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080897 restraints weight = 16412.085| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20209 Z= 0.146 Angle : 0.794 15.865 27424 Z= 0.374 Chirality : 0.046 0.530 3102 Planarity : 0.004 0.048 3454 Dihedral : 7.542 82.204 2805 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.31 % Allowed : 20.75 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2436 helix: 0.17 (0.15), residues: 1372 sheet: -2.76 (0.60), residues: 68 loop : -2.71 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 629 HIS 0.005 0.001 HIS A 587 PHE 0.033 0.001 PHE B 162 TYR 0.020 0.001 TYR A 324 ARG 0.007 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 760) hydrogen bonds : angle 4.38091 ( 2220) covalent geometry : bond 0.00342 (20209) covalent geometry : angle 0.79392 (27424) ********************** 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 385 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6985 (t-100) cc_final: 0.6586 (t60) REVERT: A 110 MET cc_start: 0.7734 (mtp) cc_final: 0.7310 (mmm) REVERT: A 122 HIS cc_start: 0.9299 (m90) cc_final: 0.8528 (m90) REVERT: A 125 VAL cc_start: 0.9647 (t) cc_final: 0.9423 (p) REVERT: A 130 MET cc_start: 0.8581 (ptt) cc_final: 0.8153 (ptt) REVERT: A 242 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8958 (t) REVERT: A 283 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7551 (mp) REVERT: A 302 ARG cc_start: 0.8178 (tpm170) cc_final: 0.7660 (tpm170) REVERT: A 331 MET cc_start: 0.8486 (tpp) cc_final: 0.7700 (tmm) REVERT: A 383 ASP cc_start: 0.9137 (t0) cc_final: 0.8672 (m-30) REVERT: A 435 MET cc_start: 0.8859 (mmt) cc_final: 0.7853 (mmt) REVERT: A 466 MET cc_start: 0.9426 (mtt) cc_final: 0.9151 (mmt) REVERT: A 515 GLU cc_start: 0.7483 (tp30) cc_final: 0.7035 (mm-30) REVERT: A 528 MET cc_start: 0.8752 (tpp) cc_final: 0.8418 (tpp) REVERT: A 554 MET cc_start: 0.8452 (tpt) cc_final: 0.8230 (tpt) REVERT: A 577 MET cc_start: 0.8652 (tpp) cc_final: 0.8376 (tpp) REVERT: A 608 LEU cc_start: 0.9418 (mp) cc_final: 0.9096 (tt) REVERT: A 635 ASP cc_start: 0.8635 (t0) cc_final: 0.8370 (t0) REVERT: B 29 TRP cc_start: 0.7006 (t-100) cc_final: 0.6607 (t60) REVERT: B 113 GLU cc_start: 0.9419 (tt0) cc_final: 0.9099 (tp30) REVERT: B 125 VAL cc_start: 0.9556 (t) cc_final: 0.9341 (p) REVERT: B 139 ARG cc_start: 0.9602 (mpt180) cc_final: 0.9295 (mmt90) REVERT: B 176 GLU cc_start: 0.9346 (pm20) cc_final: 0.9057 (pm20) REVERT: B 242 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9043 (t) REVERT: B 260 MET cc_start: 0.8891 (mmm) cc_final: 0.8669 (tpp) REVERT: B 283 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7624 (mp) REVERT: B 302 ARG cc_start: 0.8506 (tpm170) cc_final: 0.8229 (tpm170) REVERT: B 318 SER cc_start: 0.9796 (t) cc_final: 0.9534 (p) REVERT: B 331 MET cc_start: 0.8494 (tpp) cc_final: 0.7696 (tmm) REVERT: B 345 MET cc_start: 0.8782 (tpp) cc_final: 0.8574 (tpp) REVERT: B 383 ASP cc_start: 0.9099 (t0) cc_final: 0.8572 (m-30) REVERT: B 435 MET cc_start: 0.8934 (mmt) cc_final: 0.7984 (mmm) REVERT: B 554 MET cc_start: 0.8409 (tpt) cc_final: 0.8147 (tpt) REVERT: B 577 MET cc_start: 0.8571 (tpp) cc_final: 0.8083 (tpp) REVERT: B 603 MET cc_start: 0.8796 (ppp) cc_final: 0.8528 (ppp) REVERT: B 608 LEU cc_start: 0.9399 (mp) cc_final: 0.9077 (tt) REVERT: B 635 ASP cc_start: 0.8640 (t0) cc_final: 0.8387 (t0) REVERT: C 29 TRP cc_start: 0.6973 (t-100) cc_final: 0.6638 (t60) REVERT: C 78 MET cc_start: 0.8447 (ptp) cc_final: 0.8070 (pmm) REVERT: C 122 HIS cc_start: 0.9230 (m90) cc_final: 0.8787 (m-70) REVERT: C 173 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8186 (p) REVERT: C 176 GLU cc_start: 0.9387 (pm20) cc_final: 0.9125 (pm20) REVERT: C 283 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 318 SER cc_start: 0.9795 (t) cc_final: 0.9531 (p) REVERT: C 331 MET cc_start: 0.8509 (tpp) cc_final: 0.7703 (tmm) REVERT: C 345 MET cc_start: 0.8821 (tpp) cc_final: 0.8595 (tpp) REVERT: C 383 ASP cc_start: 0.9105 (t0) cc_final: 0.8576 (m-30) REVERT: C 435 MET cc_start: 0.8925 (mmt) cc_final: 0.7938 (mmm) REVERT: C 442 MET cc_start: 0.9076 (tpp) cc_final: 0.8689 (mmm) REVERT: C 515 GLU cc_start: 0.7556 (tp30) cc_final: 0.7295 (mm-30) REVERT: C 577 MET cc_start: 0.8578 (tpp) cc_final: 0.7923 (tpp) REVERT: C 635 ASP cc_start: 0.8543 (t0) cc_final: 0.8138 (t0) REVERT: D 29 TRP cc_start: 0.6999 (t-100) cc_final: 0.6610 (t60) REVERT: D 66 LYS cc_start: 0.9532 (tppt) cc_final: 0.9071 (tptp) REVERT: D 110 MET cc_start: 0.7512 (mtp) cc_final: 0.6747 (mmt) REVERT: D 130 MET cc_start: 0.8651 (ptt) cc_final: 0.8151 (ptt) REVERT: D 177 GLU cc_start: 0.9224 (pm20) cc_final: 0.8877 (pm20) REVERT: D 178 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.8983 (mm) REVERT: D 215 MET cc_start: 0.9141 (mmt) cc_final: 0.8923 (mmp) REVERT: D 315 GLU cc_start: 0.9117 (tp30) cc_final: 0.8725 (tp30) REVERT: D 318 SER cc_start: 0.9768 (t) cc_final: 0.9492 (p) REVERT: D 331 MET cc_start: 0.8513 (tpp) cc_final: 0.7791 (tmm) REVERT: D 383 ASP cc_start: 0.9035 (t0) cc_final: 0.8641 (m-30) REVERT: D 390 LEU cc_start: 0.9489 (mm) cc_final: 0.9251 (mm) REVERT: D 435 MET cc_start: 0.8812 (mmt) cc_final: 0.7833 (mmt) REVERT: D 466 MET cc_start: 0.9442 (mtt) cc_final: 0.8979 (mmm) REVERT: D 554 MET cc_start: 0.8415 (tpt) cc_final: 0.8149 (tpt) REVERT: D 603 MET cc_start: 0.8875 (ttt) cc_final: 0.8367 (tmm) REVERT: D 635 ASP cc_start: 0.8571 (t0) cc_final: 0.8296 (t0) outliers start: 49 outliers final: 29 residues processed: 366 average time/residue: 0.2674 time to fit residues: 159.1314 Evaluate side-chains 367 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 587 HIS 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 283 ILE Chi-restraints excluded: chain C residue 499 VAL 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 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 604 LEU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 138 optimal weight: 0.0370 chunk 231 optimal weight: 0.0870 chunk 145 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 81 optimal weight: 0.0000 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.100452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078665 restraints weight = 54164.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081933 restraints weight = 26481.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084207 restraints weight = 16267.480| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20209 Z= 0.124 Angle : 0.799 13.854 27424 Z= 0.373 Chirality : 0.044 0.339 3102 Planarity : 0.004 0.051 3454 Dihedral : 6.987 72.132 2805 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.60 % Allowed : 21.70 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2436 helix: 0.10 (0.15), residues: 1372 sheet: -2.66 (0.59), residues: 68 loop : -2.71 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 629 HIS 0.005 0.001 HIS A 587 PHE 0.030 0.001 PHE B 162 TYR 0.022 0.001 TYR C 324 ARG 0.006 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 760) hydrogen bonds : angle 4.24104 ( 2220) covalent geometry : bond 0.00283 (20209) covalent geometry : angle 0.79941 (27424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7856.55 seconds wall clock time: 141 minutes 5.80 seconds (8465.80 seconds total)