Starting phenix.real_space_refine on Thu Sep 18 18:26:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0p_43711/09_2025/8w0p_43711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0p_43711/09_2025/8w0p_43711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w0p_43711/09_2025/8w0p_43711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0p_43711/09_2025/8w0p_43711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w0p_43711/09_2025/8w0p_43711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0p_43711/09_2025/8w0p_43711.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 12249 2.51 5 N 3166 2.21 5 O 3673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19116 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7573 Classifications: {'peptide': 916} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 887} Chain: "B" Number of atoms: 7592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 916, 7573 Classifications: {'peptide': 916} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 887} Conformer: "B" Number of residues, atoms: 916, 7573 Classifications: {'peptide': 916} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 887} bond proxies already assigned to first conformer: 7704 Chain: "C" Number of atoms: 3897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3869 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 456} Conformer: "B" Number of residues, atoms: 475, 3869 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 456} bond proxies already assigned to first conformer: 3909 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS B 441 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 441 " occ=0.50 residue: pdb=" N AARG C 6 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 6 " occ=0.50 residue: pdb=" N AARG C 265 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 265 " occ=0.50 residue: pdb=" N ACYS C 282 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 282 " occ=0.50 Time building chain proxies: 6.10, per 1000 atoms: 0.32 Number of scatterers: 19116 At special positions: 0 Unit cell: (91.715, 158.613, 170.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 3673 8.00 N 3166 7.00 C 12249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4388 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 26 sheets defined 50.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.163A pdb=" N ARG A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 removed outlier: 4.080A pdb=" N ILE A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.718A pdb=" N GLY A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.560A pdb=" N LYS A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.660A pdb=" N SER A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.671A pdb=" N ILE A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 removed outlier: 4.478A pdb=" N LEU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.958A pdb=" N LYS A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 4.178A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 4.754A pdb=" N ILE A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.613A pdb=" N LYS A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.560A pdb=" N TYR A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 457 through 472 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 561 removed outlier: 3.806A pdb=" N TYR A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.588A pdb=" N LYS A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 removed outlier: 3.792A pdb=" N THR A 605 " --> pdb=" O PRO A 602 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 606' Processing helix chain 'A' and resid 623 through 658 removed outlier: 3.638A pdb=" N GLU A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 677 through 689 removed outlier: 3.862A pdb=" N ILE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 710 through 718 removed outlier: 3.501A pdb=" N SER A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.685A pdb=" N GLU A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 817 removed outlier: 3.587A pdb=" N SER A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 860 removed outlier: 4.289A pdb=" N ILE A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 883 Processing helix chain 'A' and resid 904 through 913 removed outlier: 3.592A pdb=" N GLU A 908 " --> pdb=" O LYS A 904 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 913 " --> pdb=" O ILE A 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 removed outlier: 3.690A pdb=" N ARG B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 4.196A pdb=" N ILE B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 removed outlier: 3.949A pdb=" N LYS B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ALA B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.617A pdb=" N PHE B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.670A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.924A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 401 through 417 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 535 through 540 removed outlier: 4.067A pdb=" N ARG B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 removed outlier: 3.826A pdb=" N GLU B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.542A pdb=" N PHE B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 656 removed outlier: 3.559A pdb=" N TYR B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 675 Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 694 through 700 removed outlier: 3.976A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 710 through 718 Processing helix chain 'B' and resid 730 through 742 removed outlier: 3.818A pdb=" N GLU B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 816 removed outlier: 3.594A pdb=" N VAL B 785 " --> pdb=" O ASP B 781 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER B 788 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 789 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 860 removed outlier: 4.998A pdb=" N LYS B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 872 removed outlier: 4.282A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 883 Processing helix chain 'B' and resid 904 through 913 removed outlier: 3.583A pdb=" N GLU B 908 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 913 " --> pdb=" O ILE B 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.643A pdb=" N SER C 14 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU C 15 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.535A pdb=" N LEU C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.745A pdb=" N ARG C 82 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 95 removed outlier: 4.599A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 143 through 154 Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 173 through 180 removed outlier: 3.531A pdb=" N ILE C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 193 Processing helix chain 'C' and resid 193 through 215 Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.577A pdb=" N SER C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.794A pdb=" N LEU C 316 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.606A pdb=" N ALA C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 410 removed outlier: 3.856A pdb=" N TYR C 405 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 removed outlier: 4.032A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 476 removed outlier: 3.733A pdb=" N GLN C 452 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.888A pdb=" N LYS A 74 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 89 " --> pdb=" O LYS A 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 149 Processing sheet with id=AA6, first strand: chain 'A' and resid 478 through 479 removed outlier: 7.896A pdb=" N PHE A 479 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY A 453 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 393 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 454 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP A 395 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP A 518 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY A 566 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 removed outlier: 7.896A pdb=" N PHE A 479 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY A 453 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 393 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 454 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP A 395 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP A 518 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY A 566 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N THR A 614 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER A 600 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 616 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 598 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 618 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 596 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 503 through 504 Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 775 removed outlier: 7.301A pdb=" N ASP A 894 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB2, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AB3, first strand: chain 'B' and resid 70 through 71 removed outlier: 5.811A pdb=" N PHE B 101 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 142 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE B 103 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 144 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 105 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N VAL B 146 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 75 removed outlier: 3.901A pdb=" N LYS B 74 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 89 " --> pdb=" O LYS B 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 78 through 80 Processing sheet with id=AB6, first strand: chain 'B' and resid 393 through 394 removed outlier: 6.515A pdb=" N ASP B 518 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLY B 569 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 520 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 571 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER B 522 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 566 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 620 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL B 595 " --> pdb=" O GLN B 620 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS B 596 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 453 through 454 removed outlier: 6.441A pdb=" N GLY B 453 " --> pdb=" O PHE B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 503 through 504 Processing sheet with id=AB9, first strand: chain 'B' and resid 756 through 758 Processing sheet with id=AC1, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AC2, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AC4, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AC5, first strand: chain 'C' and resid 283 through 285 Processing sheet with id=AC6, first strand: chain 'C' and resid 290 through 295 removed outlier: 4.157A pdb=" N LEU C 347 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 308 through 310 removed outlier: 4.183A pdb=" N LYS C 328 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 352 through 353 857 hydrogen bonds defined for protein. 2453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5733 1.34 - 1.45: 2871 1.45 - 1.57: 10850 1.57 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 19506 Sorted by residual: bond pdb=" C2 SAM B1001 " pdb=" N3 SAM B1001 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" C2 SAM A1001 " pdb=" N3 SAM A1001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C SER A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.19e-02 7.06e+03 7.51e+00 bond pdb=" C8 SAM A1001 " pdb=" N7 SAM A1001 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C8 SAM B1001 " pdb=" N7 SAM B1001 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.09e+00 ... (remaining 19501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 25701 1.76 - 3.52: 492 3.52 - 5.29: 79 5.29 - 7.05: 21 7.05 - 8.81: 9 Bond angle restraints: 26302 Sorted by residual: angle pdb=" N GLU C 456 " pdb=" CA GLU C 456 " pdb=" CB GLU C 456 " ideal model delta sigma weight residual 110.28 117.40 -7.12 1.55e+00 4.16e-01 2.11e+01 angle pdb=" C ILE C 455 " pdb=" N GLU C 456 " pdb=" CA GLU C 456 " ideal model delta sigma weight residual 120.31 113.36 6.95 1.52e+00 4.33e-01 2.09e+01 angle pdb=" C GLY B 509 " pdb=" N ASP B 510 " pdb=" CA ASP B 510 " ideal model delta sigma weight residual 125.66 133.62 -7.96 1.85e+00 2.92e-01 1.85e+01 angle pdb=" CA PRO A 273 " pdb=" N PRO A 273 " pdb=" CD PRO A 273 " ideal model delta sigma weight residual 112.00 106.15 5.85 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA PRO B 660 " pdb=" N PRO B 660 " pdb=" CD PRO B 660 " ideal model delta sigma weight residual 112.00 106.88 5.12 1.40e+00 5.10e-01 1.34e+01 ... (remaining 26297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10624 17.71 - 35.41: 1032 35.41 - 53.12: 200 53.12 - 70.83: 47 70.83 - 88.54: 20 Dihedral angle restraints: 11923 sinusoidal: 5112 harmonic: 6811 Sorted by residual: dihedral pdb=" CA LEU B 288 " pdb=" C LEU B 288 " pdb=" N ARG B 289 " pdb=" CA ARG B 289 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLU A 346 " pdb=" C GLU A 346 " pdb=" N SER A 347 " pdb=" CA SER A 347 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ARG B 286 " pdb=" C ARG B 286 " pdb=" N ALA B 287 " pdb=" CA ALA B 287 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 11920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1890 0.036 - 0.073: 702 0.073 - 0.109: 202 0.109 - 0.145: 45 0.145 - 0.182: 7 Chirality restraints: 2846 Sorted by residual: chirality pdb=" C2' SAM A1001 " pdb=" C1' SAM A1001 " pdb=" C3' SAM A1001 " pdb=" O2' SAM A1001 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CB THR B 579 " pdb=" CA THR B 579 " pdb=" OG1 THR B 579 " pdb=" CG2 THR B 579 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" C2' SAM B1001 " pdb=" C1' SAM B1001 " pdb=" C3' SAM B1001 " pdb=" O2' SAM B1001 " both_signs ideal model delta sigma weight residual False -2.76 -2.58 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 2843 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 272 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 273 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 659 " -0.054 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO B 660 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 660 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 660 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 311 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 312 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.028 5.00e-02 4.00e+02 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 547 2.71 - 3.25: 19744 3.25 - 3.80: 29427 3.80 - 4.35: 38531 4.35 - 4.90: 64025 Nonbonded interactions: 152274 Sorted by model distance: nonbonded pdb=" O GLY B 358 " pdb=" O3' SAM B1001 " model vdw 2.158 3.040 nonbonded pdb=" O PRO B 777 " pdb=" OH TYR B 861 " model vdw 2.175 3.040 nonbonded pdb=" O SER A 575 " pdb=" OG1 THR A 579 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 586 " pdb=" O SER C 17 " model vdw 2.187 3.120 nonbonded pdb=" OH TYR C 60 " pdb=" O ASP C 97 " model vdw 2.191 3.040 ... (remaining 152269 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 1 through 236 or resid 238 through 440 or resid 442 throug \ h 1001)) selection = (chain 'B' and (resid 1 through 236 or resid 238 through 440 or resid 442 throug \ h 1001)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.170 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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 : 0.003 0.089 19506 Z= 0.151 Angle : 0.626 8.809 26302 Z= 0.344 Chirality : 0.042 0.182 2846 Planarity : 0.004 0.115 3397 Dihedral : 14.727 88.535 7535 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.35 % Favored : 95.44 % Rotamer: Outliers : 0.14 % Allowed : 0.19 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2314 helix: 0.85 (0.17), residues: 984 sheet: -0.15 (0.34), residues: 229 loop : -0.87 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 244 TYR 0.020 0.001 TYR B 651 PHE 0.015 0.001 PHE A 882 TRP 0.024 0.002 TRP A 665 HIS 0.005 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00319 (19506) covalent geometry : angle 0.62635 (26302) hydrogen bonds : bond 0.15499 ( 851) hydrogen bonds : angle 6.71380 ( 2453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1707 time to fit residues: 14.8632 Evaluate side-chains 29 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.114074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.073996 restraints weight = 169810.892| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 9.35 r_work: 0.2860 rms_B_bonded: 7.47 restraints_weight: 2.0000 r_work: 0.3007 rms_B_bonded: 6.16 restraints_weight: 4.0000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19506 Z= 0.132 Angle : 0.556 8.956 26302 Z= 0.298 Chirality : 0.042 0.198 2846 Planarity : 0.004 0.072 3397 Dihedral : 5.598 59.528 2593 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 0.43 % Allowed : 3.85 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.17), residues: 2314 helix: 1.13 (0.17), residues: 1010 sheet: 0.07 (0.35), residues: 227 loop : -0.77 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 659 TYR 0.042 0.001 TYR C 262 PHE 0.014 0.001 PHE C 22 TRP 0.011 0.001 TRP A 665 HIS 0.006 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00293 (19506) covalent geometry : angle 0.55550 (26302) hydrogen bonds : bond 0.04223 ( 851) hydrogen bonds : angle 4.86585 ( 2453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.9120 (tpp) cc_final: 0.8885 (tpt) REVERT: A 468 MET cc_start: 0.9402 (mmm) cc_final: 0.9195 (mmm) REVERT: B 438 MET cc_start: 0.8874 (mmm) cc_final: 0.8250 (mmm) REVERT: C 86 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8735 (t0) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.1326 time to fit residues: 8.5827 Evaluate side-chains 33 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain C residue 86 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 65 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.113885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070552 restraints weight = 198975.044| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 12.21 r_work: 0.2846 rms_B_bonded: 10.00 restraints_weight: 2.0000 r_work: 0.2926 rms_B_bonded: 8.91 restraints_weight: 4.0000 r_work: 0.3199 rms_B_bonded: 6.75 restraints_weight: 8.0000 r_work: 0.3575 rms_B_bonded: 5.46 restraints_weight: 16.0000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19506 Z= 0.121 Angle : 0.516 9.761 26302 Z= 0.276 Chirality : 0.041 0.168 2846 Planarity : 0.004 0.057 3397 Dihedral : 5.448 58.357 2593 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.91 % Favored : 95.87 % Rotamer: Outliers : 0.57 % Allowed : 5.27 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.18), residues: 2314 helix: 1.32 (0.17), residues: 1008 sheet: 0.22 (0.35), residues: 226 loop : -0.74 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 659 TYR 0.016 0.001 TYR C 24 PHE 0.014 0.001 PHE C 22 TRP 0.012 0.001 TRP A 665 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00272 (19506) covalent geometry : angle 0.51572 (26302) hydrogen bonds : bond 0.03851 ( 851) hydrogen bonds : angle 4.56483 ( 2453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 MET cc_start: 0.9192 (mmm) cc_final: 0.8889 (mmm) REVERT: B 438 MET cc_start: 0.8419 (mmm) cc_final: 0.7916 (mmm) outliers start: 9 outliers final: 5 residues processed: 37 average time/residue: 0.1536 time to fit residues: 9.6659 Evaluate side-chains 35 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 84 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 chunk 141 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 265 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.112344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072134 restraints weight = 178199.380| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 8.87 r_work: 0.2827 rms_B_bonded: 7.19 restraints_weight: 2.0000 r_work: 0.2966 rms_B_bonded: 5.47 restraints_weight: 4.0000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 19506 Z= 0.172 Angle : 0.541 9.549 26302 Z= 0.289 Chirality : 0.042 0.171 2846 Planarity : 0.004 0.047 3397 Dihedral : 5.617 58.912 2593 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.65 % Favored : 95.22 % Rotamer: Outliers : 0.85 % Allowed : 5.94 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2314 helix: 1.40 (0.17), residues: 1013 sheet: 0.30 (0.35), residues: 225 loop : -0.72 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 659 TYR 0.037 0.001 TYR C 262 PHE 0.017 0.001 PHE C 22 TRP 0.019 0.001 TRP A 665 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00402 (19506) covalent geometry : angle 0.54111 (26302) hydrogen bonds : bond 0.03926 ( 851) hydrogen bonds : angle 4.53035 ( 2453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9093 (mp0) REVERT: A 366 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9144 (mp) REVERT: A 468 MET cc_start: 0.9469 (mmm) cc_final: 0.9024 (mmm) REVERT: B 438 MET cc_start: 0.9069 (mmm) cc_final: 0.8413 (mmm) REVERT: C 337 MET cc_start: 0.8656 (mpp) cc_final: 0.8410 (mpp) REVERT: C 456 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8289 (pp20) outliers start: 15 outliers final: 8 residues processed: 44 average time/residue: 0.1523 time to fit residues: 10.9978 Evaluate side-chains 38 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 228 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 203 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 227 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.113391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073809 restraints weight = 160025.579| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 8.72 r_work: 0.2867 rms_B_bonded: 7.38 restraints_weight: 2.0000 r_work: 0.3013 rms_B_bonded: 5.55 restraints_weight: 4.0000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 19506 Z= 0.107 Angle : 0.488 8.521 26302 Z= 0.263 Chirality : 0.041 0.159 2846 Planarity : 0.003 0.041 3397 Dihedral : 5.403 57.822 2593 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 0.90 % Allowed : 6.46 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2314 helix: 1.49 (0.17), residues: 1025 sheet: 0.34 (0.35), residues: 227 loop : -0.71 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 659 TYR 0.017 0.001 TYR C 24 PHE 0.014 0.001 PHE C 22 TRP 0.017 0.001 TRP A 665 HIS 0.002 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00237 (19506) covalent geometry : angle 0.48770 (26302) hydrogen bonds : bond 0.03511 ( 851) hydrogen bonds : angle 4.33300 ( 2453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9205 (mp0) REVERT: A 366 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9061 (mp) REVERT: A 468 MET cc_start: 0.9412 (mmm) cc_final: 0.9056 (mmm) REVERT: B 438 MET cc_start: 0.9099 (mmm) cc_final: 0.8417 (mmm) REVERT: C 79 PHE cc_start: 0.8775 (m-80) cc_final: 0.8313 (m-80) REVERT: C 86 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8825 (t0) REVERT: C 337 MET cc_start: 0.8670 (mpp) cc_final: 0.8400 (mpp) outliers start: 16 outliers final: 8 residues processed: 46 average time/residue: 0.1403 time to fit residues: 10.8509 Evaluate side-chains 40 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 157 optimal weight: 0.0050 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 149 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.113657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070752 restraints weight = 194263.031| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 10.84 r_work: 0.2852 rms_B_bonded: 8.41 restraints_weight: 2.0000 r_work: 0.2971 rms_B_bonded: 7.06 restraints_weight: 4.0000 r_work: 0.3134 rms_B_bonded: 5.57 restraints_weight: 8.0000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 19506 Z= 0.119 Angle : 0.493 8.536 26302 Z= 0.264 Chirality : 0.040 0.154 2846 Planarity : 0.003 0.041 3397 Dihedral : 5.373 57.842 2593 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.48 % Rotamer: Outliers : 0.85 % Allowed : 7.50 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2314 helix: 1.59 (0.17), residues: 1019 sheet: 0.28 (0.35), residues: 237 loop : -0.68 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 659 TYR 0.017 0.001 TYR C 24 PHE 0.015 0.001 PHE A 345 TRP 0.016 0.001 TRP A 665 HIS 0.002 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00273 (19506) covalent geometry : angle 0.49279 (26302) hydrogen bonds : bond 0.03493 ( 851) hydrogen bonds : angle 4.28174 ( 2453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9438 (OUTLIER) cc_final: 0.9160 (mp0) REVERT: A 366 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 468 MET cc_start: 0.9287 (mmm) cc_final: 0.8852 (mmm) REVERT: B 438 MET cc_start: 0.8877 (mmm) cc_final: 0.8178 (mmm) REVERT: B 468 MET cc_start: 0.8457 (ttp) cc_final: 0.8221 (tmm) REVERT: C 337 MET cc_start: 0.8352 (mpp) cc_final: 0.8146 (mpp) REVERT: C 456 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8079 (pp20) outliers start: 15 outliers final: 10 residues processed: 44 average time/residue: 0.1600 time to fit residues: 11.6415 Evaluate side-chains 42 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.111797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072173 restraints weight = 167937.003| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 8.46 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 19506 Z= 0.174 Angle : 0.528 9.394 26302 Z= 0.282 Chirality : 0.041 0.163 2846 Planarity : 0.003 0.040 3397 Dihedral : 5.613 59.296 2593 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.61 % Favored : 95.22 % Rotamer: Outliers : 0.90 % Allowed : 7.98 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.18), residues: 2314 helix: 1.53 (0.17), residues: 1021 sheet: 0.25 (0.34), residues: 237 loop : -0.70 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 659 TYR 0.020 0.001 TYR C 24 PHE 0.017 0.001 PHE C 22 TRP 0.021 0.001 TRP A 665 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00408 (19506) covalent geometry : angle 0.52814 (26302) hydrogen bonds : bond 0.03785 ( 851) hydrogen bonds : angle 4.38865 ( 2453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9094 (mp0) REVERT: A 366 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9097 (mp) REVERT: A 468 MET cc_start: 0.9233 (mmm) cc_final: 0.8971 (mmm) REVERT: B 438 MET cc_start: 0.9079 (mmm) cc_final: 0.8385 (mmm) REVERT: B 908 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: C 337 MET cc_start: 0.8866 (mpp) cc_final: 0.8567 (mpp) outliers start: 16 outliers final: 9 residues processed: 46 average time/residue: 0.1481 time to fit residues: 11.5013 Evaluate side-chains 40 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 105 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 95 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN B 293 ASN ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.112680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074111 restraints weight = 146725.613| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 9.13 r_work: 0.2822 rms_B_bonded: 8.07 restraints_weight: 2.0000 r_work: 0.2880 rms_B_bonded: 7.08 restraints_weight: 4.0000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 19506 Z= 0.112 Angle : 0.490 8.235 26302 Z= 0.263 Chirality : 0.041 0.153 2846 Planarity : 0.003 0.042 3397 Dihedral : 5.428 58.398 2593 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.39 % Favored : 95.44 % Rotamer: Outliers : 0.85 % Allowed : 8.12 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.18), residues: 2314 helix: 1.62 (0.17), residues: 1023 sheet: 0.40 (0.35), residues: 229 loop : -0.68 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 659 TYR 0.018 0.001 TYR C 24 PHE 0.015 0.001 PHE C 22 TRP 0.016 0.001 TRP A 665 HIS 0.002 0.000 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00254 (19506) covalent geometry : angle 0.48954 (26302) hydrogen bonds : bond 0.03443 ( 851) hydrogen bonds : angle 4.22855 ( 2453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9250 (mp0) REVERT: A 366 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9129 (mp) REVERT: A 468 MET cc_start: 0.9389 (mmm) cc_final: 0.9036 (mmm) REVERT: B 438 MET cc_start: 0.9252 (mmm) cc_final: 0.8640 (mmm) REVERT: B 908 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: C 337 MET cc_start: 0.8784 (mpp) cc_final: 0.8491 (mpp) outliers start: 15 outliers final: 10 residues processed: 43 average time/residue: 0.1532 time to fit residues: 11.0196 Evaluate side-chains 41 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 214 optimal weight: 6.9990 chunk 168 optimal weight: 0.4980 chunk 121 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.111130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071047 restraints weight = 183586.356| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 9.79 r_work: 0.2776 rms_B_bonded: 7.83 restraints_weight: 2.0000 r_work: 0.2892 rms_B_bonded: 5.97 restraints_weight: 4.0000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 19506 Z= 0.202 Angle : 0.550 9.710 26302 Z= 0.294 Chirality : 0.042 0.164 2846 Planarity : 0.003 0.041 3397 Dihedral : 5.698 59.634 2593 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.78 % Favored : 95.05 % Rotamer: Outliers : 0.76 % Allowed : 8.40 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2314 helix: 1.54 (0.17), residues: 1018 sheet: 0.33 (0.35), residues: 235 loop : -0.69 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 207 TYR 0.020 0.001 TYR C 24 PHE 0.018 0.001 PHE C 22 TRP 0.025 0.001 TRP A 665 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00475 (19506) covalent geometry : angle 0.54991 (26302) hydrogen bonds : bond 0.03861 ( 851) hydrogen bonds : angle 4.41982 ( 2453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: A 366 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9202 (mp) REVERT: A 468 MET cc_start: 0.9444 (mmm) cc_final: 0.9114 (mmm) REVERT: B 438 MET cc_start: 0.9308 (mmm) cc_final: 0.8785 (mmm) REVERT: B 748 MET cc_start: 0.8712 (mtp) cc_final: 0.8428 (ttt) REVERT: B 908 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: C 337 MET cc_start: 0.8814 (mpp) cc_final: 0.8548 (mpp) outliers start: 13 outliers final: 10 residues processed: 40 average time/residue: 0.1503 time to fit residues: 10.4529 Evaluate side-chains 40 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 143 optimal weight: 0.0000 chunk 172 optimal weight: 0.0020 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 195 optimal weight: 0.2980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.113194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073059 restraints weight = 134063.483| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 8.17 r_work: 0.2870 rms_B_bonded: 8.06 restraints_weight: 2.0000 r_work: 0.2990 rms_B_bonded: 5.55 restraints_weight: 4.0000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 19506 Z= 0.096 Angle : 0.483 7.676 26302 Z= 0.259 Chirality : 0.040 0.149 2846 Planarity : 0.003 0.042 3397 Dihedral : 5.328 56.139 2593 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Rotamer: Outliers : 0.90 % Allowed : 8.26 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2314 helix: 1.70 (0.17), residues: 1025 sheet: 0.30 (0.34), residues: 237 loop : -0.67 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 536 TYR 0.017 0.001 TYR C 24 PHE 0.014 0.001 PHE C 22 TRP 0.019 0.001 TRP A 665 HIS 0.002 0.000 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00204 (19506) covalent geometry : angle 0.48312 (26302) hydrogen bonds : bond 0.03300 ( 851) hydrogen bonds : angle 4.17156 ( 2453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.767 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: A 346 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.9154 (mp0) REVERT: A 366 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9084 (mp) REVERT: A 663 LYS cc_start: 0.8956 (tptp) cc_final: 0.8677 (tptp) REVERT: B 438 MET cc_start: 0.9046 (mmm) cc_final: 0.8343 (mmm) REVERT: B 908 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: C 25 MET cc_start: 0.9115 (mmm) cc_final: 0.8744 (mmt) REVERT: C 337 MET cc_start: 0.8821 (mpp) cc_final: 0.8584 (mpp) outliers start: 16 outliers final: 8 residues processed: 46 average time/residue: 0.1589 time to fit residues: 12.0328 Evaluate side-chains 40 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 0.0670 chunk 159 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 96 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.112966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073044 restraints weight = 200102.325| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 10.73 r_work: 0.2823 rms_B_bonded: 9.25 restraints_weight: 2.0000 r_work: 0.2929 rms_B_bonded: 6.75 restraints_weight: 4.0000 r_work: 0.3113 rms_B_bonded: 5.35 restraints_weight: 8.0000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 19506 Z= 0.102 Angle : 0.487 11.064 26302 Z= 0.260 Chirality : 0.040 0.148 2846 Planarity : 0.003 0.043 3397 Dihedral : 5.264 56.106 2593 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 0.66 % Allowed : 8.50 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2314 helix: 1.72 (0.17), residues: 1026 sheet: 0.10 (0.34), residues: 248 loop : -0.65 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 536 TYR 0.014 0.001 TYR C 24 PHE 0.012 0.001 PHE A 345 TRP 0.021 0.001 TRP A 665 HIS 0.002 0.000 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00231 (19506) covalent geometry : angle 0.48698 (26302) hydrogen bonds : bond 0.03284 ( 851) hydrogen bonds : angle 4.10995 ( 2453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11356.90 seconds wall clock time: 193 minutes 9.81 seconds (11589.81 seconds total)