Starting phenix.real_space_refine on Wed Mar 4 12:16:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ai5_11791/03_2026/7ai5_11791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai5_11791/03_2026/7ai5_11791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ai5_11791/03_2026/7ai5_11791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai5_11791/03_2026/7ai5_11791.map" model { file = "/net/cci-nas-00/data/ceres_data/7ai5_11791/03_2026/7ai5_11791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai5_11791/03_2026/7ai5_11791.cif" } resolution = 4.4 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 58 5.16 5 C 8258 2.51 5 N 2382 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13376 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6206 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain breaks: 1 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6206 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain breaks: 1 Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 457 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.23 Number of scatterers: 13376 At special positions: 0 Unit cell: (127.53, 128.7, 115.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 50 15.00 O 2628 8.00 N 2382 7.00 C 8258 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: 1.20 Conformation dependent library (CDL) restraints added in 385.7 milliseconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 51.3% alpha, 13.0% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.682A pdb=" N HIS A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.824A pdb=" N TYR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 186 through 191 removed outlier: 4.257A pdb=" N ILE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.646A pdb=" N ALA A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.597A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.843A pdb=" N VAL A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.889A pdb=" N LEU A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 344 Proline residue: A 340 - end of helix removed outlier: 3.927A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 361 through 385 removed outlier: 3.657A pdb=" N ARG A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 376 - end of helix removed outlier: 3.796A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.506A pdb=" N GLN A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.899A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 removed outlier: 3.901A pdb=" N TYR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 536 removed outlier: 3.848A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 removed outlier: 4.215A pdb=" N GLU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.848A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.730A pdb=" N THR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 716 removed outlier: 3.943A pdb=" N SER A 706 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.563A pdb=" N LYS A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 4.078A pdb=" N ALA A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'B' and resid 11 through 24 removed outlier: 3.698A pdb=" N HIS B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.816A pdb=" N TYR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 191 removed outlier: 4.323A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.638A pdb=" N ALA B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.598A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.590A pdb=" N ASN B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.883A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 Proline residue: B 340 - end of helix removed outlier: 3.948A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 361 through 385 removed outlier: 3.664A pdb=" N ARG B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 376 - end of helix removed outlier: 3.806A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.532A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 442 removed outlier: 3.955A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.887A pdb=" N TYR B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 536 removed outlier: 3.847A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 566 removed outlier: 4.299A pdb=" N GLU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 621 through 635 removed outlier: 3.659A pdb=" N THR B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.725A pdb=" N THR B 675 " --> pdb=" O MET B 671 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 716 removed outlier: 3.850A pdb=" N ALA B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 713 " --> pdb=" O TRP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.577A pdb=" N LYS B 738 " --> pdb=" O GLN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 4.045A pdb=" N ALA B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 800 removed outlier: 3.613A pdb=" N SER B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.310A pdb=" N ILE A 66 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 71 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 28 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N CYS A 93 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 30 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN A 95 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ARG A 32 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.630A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ALA A 181 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE A 136 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 135 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 155 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.952A pdb=" N ILE A 268 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR A 655 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 652 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 691 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.641A pdb=" N GLY A 466 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR A 494 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG A 500 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 572 removed outlier: 6.886A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 613 removed outlier: 6.790A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 613 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 749 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN A 744 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 763 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS A 746 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 761 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP A 748 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET A 759 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 752 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 755 " --> pdb=" O HIS A 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.273A pdb=" N GLU B 94 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL B 110 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.909A pdb=" N ILE B 66 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.619A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 134 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA B 181 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE B 136 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 135 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 137 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 155 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 468 removed outlier: 3.649A pdb=" N GLY B 466 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR B 494 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 500 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.816A pdb=" N THR B 571 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 609 through 613 removed outlier: 6.792A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 652 through 657 removed outlier: 6.313A pdb=" N ARG B 652 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU B 691 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP B 693 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 656 " --> pdb=" O ASP B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 750 through 752 removed outlier: 3.546A pdb=" N HIS B 752 " --> pdb=" O THR B 755 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 755 " --> pdb=" O HIS B 752 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2168 1.30 - 1.44: 3618 1.44 - 1.58: 7714 1.58 - 1.72: 96 1.72 - 1.86: 104 Bond restraints: 13700 Sorted by residual: bond pdb=" C ILE A 650 " pdb=" O ILE A 650 " ideal model delta sigma weight residual 1.236 1.317 -0.080 1.04e-02 9.25e+03 5.99e+01 bond pdb=" C ILE A 636 " pdb=" O ILE A 636 " ideal model delta sigma weight residual 1.242 1.309 -0.067 1.13e-02 7.83e+03 3.55e+01 bond pdb=" C THR A 685 " pdb=" O THR A 685 " ideal model delta sigma weight residual 1.238 1.177 0.061 1.06e-02 8.90e+03 3.26e+01 bond pdb=" C PRO A 175 " pdb=" O PRO A 175 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.30e-02 5.92e+03 2.87e+01 bond pdb=" C GLY A 780 " pdb=" O GLY A 780 " ideal model delta sigma weight residual 1.232 1.283 -0.051 1.03e-02 9.43e+03 2.49e+01 ... (remaining 13695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 14597 2.29 - 4.57: 3849 4.57 - 6.86: 267 6.86 - 9.14: 24 9.14 - 11.43: 9 Bond angle restraints: 18746 Sorted by residual: angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 131.11 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" C PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta sigma weight residual 110.98 99.55 11.43 1.31e+00 5.83e-01 7.61e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 131.37 8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE A 155 " pdb=" CB PHE A 155 " pdb=" CG PHE A 155 " ideal model delta sigma weight residual 113.80 121.58 -7.78 1.00e+00 1.00e+00 6.05e+01 angle pdb=" N SER A 621 " pdb=" CA SER A 621 " pdb=" C SER A 621 " ideal model delta sigma weight residual 111.14 119.34 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 18741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7149 17.99 - 35.97: 713 35.97 - 53.96: 336 53.96 - 71.95: 78 71.95 - 89.93: 22 Dihedral angle restraints: 8298 sinusoidal: 3722 harmonic: 4576 Sorted by residual: dihedral pdb=" C THR A 273 " pdb=" N THR A 273 " pdb=" CA THR A 273 " pdb=" CB THR A 273 " ideal model delta harmonic sigma weight residual -122.00 -109.90 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO A 615 " pdb=" N PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta harmonic sigma weight residual -120.70 -108.69 -12.01 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C ASN B 593 " pdb=" N ASN B 593 " pdb=" CA ASN B 593 " pdb=" CB ASN B 593 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 8295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1228 0.088 - 0.177: 731 0.177 - 0.265: 139 0.265 - 0.353: 21 0.353 - 0.442: 3 Chirality restraints: 2122 Sorted by residual: chirality pdb=" CB VAL A 640 " pdb=" CA VAL A 640 " pdb=" CG1 VAL A 640 " pdb=" CG2 VAL A 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ALA A 766 " pdb=" N ALA A 766 " pdb=" C ALA A 766 " pdb=" CB ALA A 766 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA VAL B 657 " pdb=" N VAL B 657 " pdb=" C VAL B 657 " pdb=" CB VAL B 657 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2119 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 635 " 0.021 2.00e-02 2.50e+03 3.60e-02 2.59e+01 pdb=" CG TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 635 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 635 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 635 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 635 " 0.041 2.00e-02 2.50e+03 pdb=" OH TYR A 635 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 132 " 0.022 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU A 132 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU A 132 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A 133 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 309 " -0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ARG A 309 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG A 309 " -0.027 2.00e-02 2.50e+03 pdb=" N TRP A 310 " -0.025 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 5547 2.96 - 3.44: 13307 3.44 - 3.93: 22952 3.93 - 4.41: 26036 4.41 - 4.90: 40766 Nonbonded interactions: 108608 Sorted by model distance: nonbonded pdb=" N ASN B 616 " pdb=" O ASN B 616 " model vdw 2.472 2.496 nonbonded pdb=" OD1 ASP B 296 " pdb=" OG1 THR B 298 " model vdw 2.479 3.040 nonbonded pdb=" O ASP B 98 " pdb=" OG1 THR B 101 " model vdw 2.484 3.040 nonbonded pdb=" N GLU A 731 " pdb=" OE1 GLU A 731 " model vdw 2.511 3.120 nonbonded pdb=" N TYR A 702 " pdb=" N ASP A 703 " model vdw 2.521 2.560 ... (remaining 108603 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.014 0.080 13700 Z= 1.031 Angle : 1.846 11.431 18746 Z= 1.375 Chirality : 0.104 0.442 2122 Planarity : 0.008 0.054 2288 Dihedral : 18.260 89.933 5346 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.14 % Allowed : 9.60 % Favored : 89.25 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 1568 helix: -0.83 (0.18), residues: 665 sheet: -1.88 (0.36), residues: 137 loop : -1.65 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG A 652 TYR 0.072 0.007 TYR A 635 PHE 0.070 0.006 PHE A 36 TRP 0.022 0.005 TRP A 310 HIS 0.040 0.006 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.01388 (13700) covalent geometry : angle 1.84595 (18746) hydrogen bonds : bond 0.22752 ( 629) hydrogen bonds : angle 8.08747 ( 1714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 289 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8196 (mmm) cc_final: 0.7995 (mmm) REVERT: A 187 MET cc_start: 0.8972 (mmm) cc_final: 0.8043 (mmt) REVERT: A 269 MET cc_start: 0.7066 (mtm) cc_final: 0.6796 (mmm) REVERT: A 365 LEU cc_start: 0.9283 (mt) cc_final: 0.8913 (mm) REVERT: A 574 ASP cc_start: 0.8482 (m-30) cc_final: 0.7958 (p0) REVERT: A 674 MET cc_start: 0.8911 (mmm) cc_final: 0.8248 (mmt) REVERT: A 686 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8191 (tp30) REVERT: A 730 PHE cc_start: 0.8006 (t80) cc_final: 0.7601 (t80) REVERT: B 88 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 171 GLN cc_start: 0.9430 (tt0) cc_final: 0.9138 (tt0) REVERT: B 173 THR cc_start: 0.8876 (p) cc_final: 0.8183 (p) REVERT: B 258 ILE cc_start: 0.9151 (tt) cc_final: 0.8771 (tt) REVERT: B 441 ASP cc_start: 0.7806 (m-30) cc_final: 0.7556 (p0) REVERT: B 603 LEU cc_start: 0.8852 (mt) cc_final: 0.8559 (mm) REVERT: B 616 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (m-40) REVERT: B 633 MET cc_start: 0.8694 (mtm) cc_final: 0.8272 (mtm) REVERT: B 703 ASP cc_start: 0.8564 (t70) cc_final: 0.7949 (t70) REVERT: B 730 PHE cc_start: 0.7230 (t80) cc_final: 0.6937 (t80) REVERT: B 732 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8244 (mt) outliers start: 15 outliers final: 3 residues processed: 300 average time/residue: 0.1353 time to fit residues: 55.2887 Evaluate side-chains 160 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 683 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 683 ASN B 763 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.078067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.057571 restraints weight = 84444.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.059356 restraints weight = 50228.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.060524 restraints weight = 34212.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061316 restraints weight = 25972.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.061778 restraints weight = 21460.735| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13700 Z= 0.186 Angle : 0.690 8.885 18746 Z= 0.369 Chirality : 0.044 0.227 2122 Planarity : 0.005 0.079 2288 Dihedral : 18.322 89.233 2292 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.30 % Allowed : 2.74 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1568 helix: 0.58 (0.19), residues: 716 sheet: -1.49 (0.31), residues: 195 loop : -1.30 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 404 TYR 0.021 0.002 TYR A 528 PHE 0.028 0.002 PHE A 372 TRP 0.017 0.002 TRP A 137 HIS 0.007 0.001 HIS A 585 Details of bonding type rmsd covalent geometry : bond 0.00405 (13700) covalent geometry : angle 0.69029 (18746) hydrogen bonds : bond 0.04838 ( 629) hydrogen bonds : angle 5.27731 ( 1714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9617 (mt) cc_final: 0.9399 (tp) REVERT: A 508 GLU cc_start: 0.9370 (tt0) cc_final: 0.9150 (pt0) REVERT: A 574 ASP cc_start: 0.8495 (m-30) cc_final: 0.7734 (p0) REVERT: A 575 LYS cc_start: 0.8209 (mttt) cc_final: 0.7922 (mmmt) REVERT: A 771 TYR cc_start: 0.8141 (p90) cc_final: 0.7615 (p90) REVERT: B 128 ARG cc_start: 0.6175 (mtt180) cc_final: 0.5824 (ptp-110) REVERT: B 243 TYR cc_start: 0.8544 (t80) cc_final: 0.7969 (t80) REVERT: B 441 ASP cc_start: 0.8738 (m-30) cc_final: 0.8339 (p0) REVERT: B 633 MET cc_start: 0.8786 (mtm) cc_final: 0.8432 (mtm) REVERT: B 759 MET cc_start: 0.7732 (mmt) cc_final: 0.7361 (mmt) REVERT: B 771 TYR cc_start: 0.7655 (p90) cc_final: 0.7318 (p90) outliers start: 4 outliers final: 1 residues processed: 178 average time/residue: 0.1224 time to fit residues: 30.4726 Evaluate side-chains 116 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 chunk 126 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 626 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.088300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064834 restraints weight = 70609.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.066428 restraints weight = 46880.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067473 restraints weight = 34900.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068225 restraints weight = 28350.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.068656 restraints weight = 24577.334| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13700 Z= 0.129 Angle : 0.602 7.017 18746 Z= 0.321 Chirality : 0.042 0.284 2122 Planarity : 0.005 0.055 2288 Dihedral : 18.271 89.662 2292 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1568 helix: 0.88 (0.19), residues: 721 sheet: -1.08 (0.31), residues: 206 loop : -1.20 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 656 TYR 0.018 0.001 TYR B 31 PHE 0.019 0.001 PHE A 372 TRP 0.009 0.001 TRP A 137 HIS 0.005 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00277 (13700) covalent geometry : angle 0.60248 (18746) hydrogen bonds : bond 0.04032 ( 629) hydrogen bonds : angle 4.89011 ( 1714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 CYS cc_start: 0.8573 (t) cc_final: 0.8151 (m) REVERT: A 365 LEU cc_start: 0.9617 (mm) cc_final: 0.9278 (mt) REVERT: A 445 ASP cc_start: 0.9317 (t0) cc_final: 0.8954 (p0) REVERT: A 744 ASN cc_start: 0.8684 (t0) cc_final: 0.8389 (t0) REVERT: A 745 VAL cc_start: 0.9751 (m) cc_final: 0.9491 (t) REVERT: A 771 TYR cc_start: 0.8165 (p90) cc_final: 0.7574 (p90) REVERT: B 13 MET cc_start: 0.6738 (ppp) cc_final: 0.6514 (ppp) REVERT: B 68 MET cc_start: 0.3478 (tmm) cc_final: 0.3238 (tmm) REVERT: B 629 LEU cc_start: 0.7809 (mt) cc_final: 0.7346 (mt) REVERT: B 633 MET cc_start: 0.8622 (mtm) cc_final: 0.8109 (mtm) REVERT: B 717 ASN cc_start: 0.8863 (m-40) cc_final: 0.8621 (m-40) REVERT: B 771 TYR cc_start: 0.7599 (p90) cc_final: 0.7297 (p90) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1089 time to fit residues: 25.9469 Evaluate side-chains 113 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 126 GLN A 312 HIS ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 626 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 391 GLN B 616 ASN B 746 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.069589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049670 restraints weight = 89206.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.050965 restraints weight = 57225.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.051847 restraints weight = 41649.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052452 restraints weight = 33246.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.052840 restraints weight = 28399.071| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 13700 Z= 0.426 Angle : 1.015 13.207 18746 Z= 0.520 Chirality : 0.052 0.379 2122 Planarity : 0.008 0.085 2288 Dihedral : 18.967 89.965 2292 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 0.15 % Allowed : 5.03 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.19), residues: 1568 helix: -0.63 (0.17), residues: 739 sheet: -1.60 (0.31), residues: 192 loop : -1.62 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 193 TYR 0.049 0.003 TYR A 429 PHE 0.030 0.004 PHE A 532 TRP 0.013 0.003 TRP B 137 HIS 0.009 0.002 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00910 (13700) covalent geometry : angle 1.01495 (18746) hydrogen bonds : bond 0.06529 ( 629) hydrogen bonds : angle 6.03794 ( 1714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8475 (mmm) cc_final: 0.8215 (mmm) REVERT: A 187 MET cc_start: 0.8363 (mmt) cc_final: 0.8136 (mmt) REVERT: A 239 CYS cc_start: 0.8800 (t) cc_final: 0.8478 (m) REVERT: A 355 LEU cc_start: 0.9322 (tp) cc_final: 0.9115 (tp) REVERT: A 372 PHE cc_start: 0.8656 (m-80) cc_final: 0.8446 (m-80) REVERT: A 574 ASP cc_start: 0.8572 (m-30) cc_final: 0.7967 (p0) REVERT: A 617 MET cc_start: 0.8927 (mmp) cc_final: 0.8687 (mmm) REVERT: B 13 MET cc_start: 0.7414 (ppp) cc_final: 0.7175 (ppp) REVERT: B 68 MET cc_start: 0.5237 (tmm) cc_final: 0.4728 (tmm) REVERT: B 397 MET cc_start: 0.9052 (mtm) cc_final: 0.8650 (mmm) REVERT: B 441 ASP cc_start: 0.8857 (m-30) cc_final: 0.8612 (m-30) REVERT: B 633 MET cc_start: 0.9047 (mtm) cc_final: 0.8487 (mtm) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1171 time to fit residues: 21.6876 Evaluate side-chains 82 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.074189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053820 restraints weight = 85500.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.055365 restraints weight = 52422.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056380 restraints weight = 36756.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.057065 restraints weight = 28560.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.057497 restraints weight = 24014.025| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13700 Z= 0.127 Angle : 0.621 6.892 18746 Z= 0.331 Chirality : 0.043 0.169 2122 Planarity : 0.005 0.052 2288 Dihedral : 18.574 89.580 2292 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1568 helix: 0.75 (0.19), residues: 727 sheet: -1.32 (0.32), residues: 193 loop : -1.24 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 305 TYR 0.025 0.002 TYR A 528 PHE 0.011 0.001 PHE B 532 TRP 0.005 0.001 TRP B 709 HIS 0.004 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00273 (13700) covalent geometry : angle 0.62095 (18746) hydrogen bonds : bond 0.03828 ( 629) hydrogen bonds : angle 4.95350 ( 1714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8876 (tp) cc_final: 0.8584 (tp) REVERT: A 68 MET cc_start: 0.8752 (mmm) cc_final: 0.8371 (mmm) REVERT: A 306 MET cc_start: 0.9247 (tpt) cc_final: 0.9018 (tpt) REVERT: A 313 MET cc_start: 0.7825 (tpp) cc_final: 0.7576 (tpt) REVERT: A 321 LEU cc_start: 0.8685 (mt) cc_final: 0.8314 (mt) REVERT: A 372 PHE cc_start: 0.8759 (m-10) cc_final: 0.8455 (m-80) REVERT: A 445 ASP cc_start: 0.9290 (t0) cc_final: 0.9078 (t0) REVERT: A 447 LEU cc_start: 0.9585 (mp) cc_final: 0.9288 (tp) REVERT: A 574 ASP cc_start: 0.8659 (m-30) cc_final: 0.7944 (p0) REVERT: A 617 MET cc_start: 0.8868 (mmp) cc_final: 0.8633 (mmm) REVERT: A 759 MET cc_start: 0.8214 (mmm) cc_final: 0.7690 (mmm) REVERT: B 441 ASP cc_start: 0.8843 (m-30) cc_final: 0.8597 (m-30) REVERT: B 543 GLN cc_start: 0.8772 (mt0) cc_final: 0.8271 (mt0) REVERT: B 633 MET cc_start: 0.8874 (mtm) cc_final: 0.8310 (mtm) REVERT: B 771 TYR cc_start: 0.7884 (p90) cc_final: 0.7611 (p90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1117 time to fit residues: 23.0451 Evaluate side-chains 104 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 497 ASN B 557 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.073209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.052974 restraints weight = 85656.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.054462 restraints weight = 52815.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.055462 restraints weight = 37374.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.056129 restraints weight = 29239.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.056589 restraints weight = 24677.672| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13700 Z= 0.162 Angle : 0.627 7.345 18746 Z= 0.330 Chirality : 0.042 0.260 2122 Planarity : 0.005 0.056 2288 Dihedral : 18.427 88.636 2292 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1568 helix: 0.95 (0.19), residues: 729 sheet: -1.31 (0.32), residues: 191 loop : -1.25 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 305 TYR 0.024 0.002 TYR A 446 PHE 0.024 0.002 PHE B 36 TRP 0.005 0.001 TRP B 709 HIS 0.005 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00358 (13700) covalent geometry : angle 0.62711 (18746) hydrogen bonds : bond 0.03897 ( 629) hydrogen bonds : angle 4.90176 ( 1714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9025 (tp) cc_final: 0.8804 (tp) REVERT: A 68 MET cc_start: 0.8826 (mmm) cc_final: 0.8502 (mmm) REVERT: A 239 CYS cc_start: 0.8751 (t) cc_final: 0.8294 (m) REVERT: A 372 PHE cc_start: 0.8818 (m-10) cc_final: 0.8600 (m-80) REVERT: A 574 ASP cc_start: 0.8722 (m-30) cc_final: 0.7961 (p0) REVERT: A 617 MET cc_start: 0.8838 (mmp) cc_final: 0.8630 (mmm) REVERT: A 674 MET cc_start: 0.8545 (mmp) cc_final: 0.8208 (mmt) REVERT: A 723 THR cc_start: 0.8301 (t) cc_final: 0.8030 (t) REVERT: A 742 VAL cc_start: 0.7413 (t) cc_final: 0.7044 (t) REVERT: B 68 MET cc_start: 0.5335 (tmm) cc_final: 0.4910 (tmm) REVERT: B 311 LEU cc_start: 0.9478 (mt) cc_final: 0.9268 (mt) REVERT: B 441 ASP cc_start: 0.8864 (m-30) cc_final: 0.8622 (m-30) REVERT: B 543 GLN cc_start: 0.8803 (mt0) cc_final: 0.8229 (mt0) REVERT: B 633 MET cc_start: 0.8904 (mtm) cc_final: 0.8326 (mtm) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.1094 time to fit residues: 22.2413 Evaluate side-chains 104 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 0.0570 chunk 71 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.074180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053864 restraints weight = 85363.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.055387 restraints weight = 53070.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.056420 restraints weight = 37480.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.057029 restraints weight = 29173.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.057572 restraints weight = 24693.621| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13700 Z= 0.124 Angle : 0.600 11.333 18746 Z= 0.318 Chirality : 0.041 0.220 2122 Planarity : 0.005 0.144 2288 Dihedral : 18.302 89.925 2292 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1568 helix: 1.15 (0.19), residues: 727 sheet: -1.16 (0.32), residues: 192 loop : -1.14 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262 TYR 0.020 0.001 TYR A 446 PHE 0.021 0.001 PHE B 36 TRP 0.005 0.001 TRP B 709 HIS 0.005 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00269 (13700) covalent geometry : angle 0.59971 (18746) hydrogen bonds : bond 0.03517 ( 629) hydrogen bonds : angle 4.74602 ( 1714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8995 (tp) cc_final: 0.8788 (tp) REVERT: A 68 MET cc_start: 0.8785 (mmm) cc_final: 0.8498 (mmm) REVERT: A 313 MET cc_start: 0.7775 (tpp) cc_final: 0.7562 (tpt) REVERT: A 372 PHE cc_start: 0.8742 (m-10) cc_final: 0.8515 (m-80) REVERT: A 574 ASP cc_start: 0.8735 (m-30) cc_final: 0.7903 (p0) REVERT: A 617 MET cc_start: 0.8700 (mmp) cc_final: 0.8250 (tpt) REVERT: A 674 MET cc_start: 0.8483 (mmp) cc_final: 0.8199 (mmt) REVERT: A 759 MET cc_start: 0.8139 (mmm) cc_final: 0.7663 (mmm) REVERT: B 241 LEU cc_start: 0.9736 (mt) cc_final: 0.9423 (tp) REVERT: B 441 ASP cc_start: 0.8839 (m-30) cc_final: 0.8596 (m-30) REVERT: B 543 GLN cc_start: 0.8772 (mt0) cc_final: 0.8287 (mt0) REVERT: B 633 MET cc_start: 0.8902 (mtm) cc_final: 0.8320 (mtm) REVERT: B 697 ARG cc_start: 0.6814 (tpt90) cc_final: 0.6357 (tpt90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1120 time to fit residues: 22.9165 Evaluate side-chains 108 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 150 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.074345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053950 restraints weight = 84550.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055463 restraints weight = 52598.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056453 restraints weight = 37201.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057156 restraints weight = 29096.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.057622 restraints weight = 24420.245| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13700 Z= 0.122 Angle : 0.586 8.613 18746 Z= 0.308 Chirality : 0.041 0.235 2122 Planarity : 0.005 0.079 2288 Dihedral : 18.160 89.707 2292 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1568 helix: 1.09 (0.19), residues: 732 sheet: -0.88 (0.35), residues: 176 loop : -1.11 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 492 TYR 0.023 0.001 TYR B 509 PHE 0.017 0.001 PHE B 36 TRP 0.007 0.001 TRP B 709 HIS 0.005 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00265 (13700) covalent geometry : angle 0.58566 (18746) hydrogen bonds : bond 0.03453 ( 629) hydrogen bonds : angle 4.66573 ( 1714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8704 (mmm) cc_final: 0.8464 (mmm) REVERT: A 306 MET cc_start: 0.9277 (tpt) cc_final: 0.8757 (tpp) REVERT: A 321 LEU cc_start: 0.8553 (mt) cc_final: 0.8336 (mt) REVERT: A 368 MET cc_start: 0.9055 (ptt) cc_final: 0.8834 (ptp) REVERT: A 372 PHE cc_start: 0.8715 (m-10) cc_final: 0.8477 (m-80) REVERT: A 574 ASP cc_start: 0.8658 (m-30) cc_final: 0.7756 (p0) REVERT: A 674 MET cc_start: 0.8490 (mmp) cc_final: 0.8248 (mmt) REVERT: A 759 MET cc_start: 0.8129 (mmm) cc_final: 0.7663 (mmm) REVERT: A 771 TYR cc_start: 0.7946 (p90) cc_final: 0.7707 (p90) REVERT: B 13 MET cc_start: 0.6820 (ppp) cc_final: 0.6559 (ppp) REVERT: B 113 ILE cc_start: 0.8644 (mp) cc_final: 0.8419 (mp) REVERT: B 241 LEU cc_start: 0.9721 (mt) cc_final: 0.9399 (tp) REVERT: B 368 MET cc_start: 0.7747 (mmt) cc_final: 0.7528 (mmm) REVERT: B 441 ASP cc_start: 0.8804 (m-30) cc_final: 0.8558 (m-30) REVERT: B 543 GLN cc_start: 0.8755 (mt0) cc_final: 0.8183 (mp10) REVERT: B 633 MET cc_start: 0.8921 (mtm) cc_final: 0.8329 (mtm) REVERT: B 697 ARG cc_start: 0.6903 (tpt90) cc_final: 0.6455 (tpt90) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1144 time to fit residues: 22.0976 Evaluate side-chains 102 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 0.0000 chunk 108 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.073440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.053114 restraints weight = 86030.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054544 restraints weight = 53257.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055513 restraints weight = 38016.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056192 restraints weight = 29866.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.056649 restraints weight = 25273.695| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13700 Z= 0.141 Angle : 0.604 9.611 18746 Z= 0.314 Chirality : 0.041 0.200 2122 Planarity : 0.005 0.062 2288 Dihedral : 18.125 89.970 2292 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1568 helix: 1.09 (0.19), residues: 732 sheet: -0.86 (0.35), residues: 191 loop : -1.04 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 367 TYR 0.018 0.001 TYR B 509 PHE 0.014 0.002 PHE B 36 TRP 0.007 0.001 TRP A 137 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00310 (13700) covalent geometry : angle 0.60364 (18746) hydrogen bonds : bond 0.03551 ( 629) hydrogen bonds : angle 4.67145 ( 1714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8641 (mmp) cc_final: 0.8176 (ptm) REVERT: A 269 MET cc_start: 0.7114 (tpp) cc_final: 0.6810 (mmt) REVERT: A 306 MET cc_start: 0.9267 (tpt) cc_final: 0.9052 (tpp) REVERT: A 313 MET cc_start: 0.8444 (tpp) cc_final: 0.8205 (tpp) REVERT: A 368 MET cc_start: 0.8968 (ptt) cc_final: 0.8726 (ptp) REVERT: A 372 PHE cc_start: 0.8792 (m-10) cc_final: 0.8567 (m-80) REVERT: A 574 ASP cc_start: 0.8691 (m-30) cc_final: 0.7747 (p0) REVERT: A 617 MET cc_start: 0.8517 (mmp) cc_final: 0.8035 (tpt) REVERT: A 674 MET cc_start: 0.8449 (mmp) cc_final: 0.8202 (mmt) REVERT: A 759 MET cc_start: 0.8232 (mmm) cc_final: 0.7849 (mmm) REVERT: B 68 MET cc_start: 0.4617 (tmm) cc_final: 0.4309 (tmm) REVERT: B 441 ASP cc_start: 0.8769 (m-30) cc_final: 0.8539 (m-30) REVERT: B 543 GLN cc_start: 0.8799 (mt0) cc_final: 0.8236 (mp10) REVERT: B 633 MET cc_start: 0.8981 (mtm) cc_final: 0.8381 (mtm) REVERT: B 697 ARG cc_start: 0.7073 (tpt90) cc_final: 0.6551 (tpt90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1081 time to fit residues: 20.1516 Evaluate side-chains 95 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.073828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053373 restraints weight = 85274.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054843 restraints weight = 53264.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055824 restraints weight = 37929.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.056504 restraints weight = 29687.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.056956 restraints weight = 25172.424| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13700 Z= 0.124 Angle : 0.602 8.193 18746 Z= 0.313 Chirality : 0.041 0.240 2122 Planarity : 0.005 0.053 2288 Dihedral : 18.091 89.849 2292 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1568 helix: 1.15 (0.19), residues: 727 sheet: -0.74 (0.37), residues: 186 loop : -0.99 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.019 0.001 TYR B 509 PHE 0.015 0.001 PHE A 143 TRP 0.006 0.001 TRP B 709 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00274 (13700) covalent geometry : angle 0.60152 (18746) hydrogen bonds : bond 0.03438 ( 629) hydrogen bonds : angle 4.60368 ( 1714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8607 (mmp) cc_final: 0.8176 (ptp) REVERT: A 269 MET cc_start: 0.6993 (tpp) cc_final: 0.6701 (mmt) REVERT: A 306 MET cc_start: 0.9277 (tpt) cc_final: 0.9057 (tpp) REVERT: A 368 MET cc_start: 0.9014 (ptt) cc_final: 0.8749 (ptp) REVERT: A 372 PHE cc_start: 0.8746 (m-10) cc_final: 0.8522 (m-80) REVERT: A 674 MET cc_start: 0.8433 (mmp) cc_final: 0.8204 (mmt) REVERT: A 759 MET cc_start: 0.8196 (mmm) cc_final: 0.7791 (mmm) REVERT: B 13 MET cc_start: 0.6846 (ppp) cc_final: 0.6572 (ppp) REVERT: B 68 MET cc_start: 0.4859 (tmm) cc_final: 0.4535 (tmm) REVERT: B 241 LEU cc_start: 0.9740 (mt) cc_final: 0.9431 (tp) REVERT: B 368 MET cc_start: 0.7556 (mmt) cc_final: 0.7216 (mmp) REVERT: B 441 ASP cc_start: 0.8773 (m-30) cc_final: 0.8531 (m-30) REVERT: B 543 GLN cc_start: 0.8660 (mt0) cc_final: 0.8155 (mp10) REVERT: B 633 MET cc_start: 0.8939 (mtm) cc_final: 0.8355 (mtm) REVERT: B 697 ARG cc_start: 0.7155 (tpt90) cc_final: 0.6661 (tpt90) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1054 time to fit residues: 19.5254 Evaluate side-chains 92 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.0370 chunk 7 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.073554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053136 restraints weight = 86044.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.054577 restraints weight = 53467.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055544 restraints weight = 38147.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.056236 restraints weight = 29913.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056684 restraints weight = 25341.895| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13700 Z= 0.127 Angle : 0.595 7.987 18746 Z= 0.310 Chirality : 0.041 0.190 2122 Planarity : 0.005 0.050 2288 Dihedral : 18.033 89.991 2292 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1568 helix: 1.16 (0.19), residues: 727 sheet: -0.60 (0.36), residues: 192 loop : -0.99 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 492 TYR 0.017 0.001 TYR B 509 PHE 0.013 0.001 PHE B 36 TRP 0.007 0.001 TRP B 709 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00282 (13700) covalent geometry : angle 0.59463 (18746) hydrogen bonds : bond 0.03466 ( 629) hydrogen bonds : angle 4.60901 ( 1714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.07 seconds wall clock time: 37 minutes 26.73 seconds (2246.73 seconds total)