Starting phenix.real_space_refine on Sat Sep 12 03:56:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ai5_11791/09_2026/7ai5_11791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai5_11791/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ai5_11791/09_2026/7ai5_11791.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ai5_11791/09_2026/7ai5_11791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ai5_11791/09_2026/7ai5_11791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai5_11791/09_2026/7ai5_11791.map" model { file = "/net/cci-nas-00/data/ceres_data/7ai5_11791/09_2026/7ai5_11791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai5_11791/09_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-2.2.1-6174/lib/python3.11/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: 3.07, 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: 1.09 Conformation dependent library (CDL) restraints added in 577.4 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: 1.64 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: 2.81 Time building geometry restraints manager: 1.45 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: 14615 2.29 - 4.57: 3830 4.57 - 6.86: 268 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: 7126 17.99 - 35.97: 701 35.97 - 53.96: 318 53.96 - 71.95: 71 71.95 - 89.93: 20 Dihedral angle restraints: 8236 sinusoidal: 3660 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 8233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1217 0.088 - 0.177: 741 0.177 - 0.265: 140 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: 1.010 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.910 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 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= 1.035 Angle : 1.844 11.431 18746 Z= 1.376 Chirality : 0.105 0.442 2122 Planarity : 0.008 0.054 2288 Dihedral : 17.870 89.933 5284 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/Z covalent geometry : bond 0.01388 / 1.04 (13700) covalent geometry : angle 1.84431 / 1.38 (18746) hydrogen bonds : bond 0.22752 / 15.18 ( 629) hydrogen bonds : angle 8.08747 / 5.52 ( 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 : 0.498 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: 0.1494 time to fit residues: 61.5749 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 : 0.511 ------------------------------------------------------------------------------- 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... A 248 GLN A 276 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 599 ASN B 616 ASN B 683 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.058153 restraints weight = 84224.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.059936 restraints weight = 49306.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.061105 restraints weight = 33516.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.061895 restraints weight = 25455.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062328 restraints weight = 20983.035| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13700 Z= 0.194 Angle : 0.748 10.818 18746 Z= 0.399 Chirality : 0.047 0.296 2122 Planarity : 0.006 0.071 2288 Dihedral : 17.674 88.221 2230 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.23 % Allowed : 2.82 % 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: -1.09 (0.19), residues: 1568 helix: 0.19 (0.18), residues: 721 sheet: -1.55 (0.31), residues: 184 loop : -1.42 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 579 TYR 0.022 0.002 TYR B 31 PHE 0.023 0.002 PHE A 372 TRP 0.021 0.003 TRP A 137 HIS 0.011 0.001 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (13700) covalent geometry : angle 0.74846 / 0.40 (18746) hydrogen bonds : bond 0.05972 / 3.99 ( 629) hydrogen bonds : angle 5.59692 / 3.81 ( 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 182 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.616 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 187 MET cc_start: 0.8900 (mmm) cc_final: 0.8626 (mmt) REVERT: A 574 ASP cc_start: 0.8450 (m-30) cc_final: 0.7690 (p0) REVERT: A 575 LYS cc_start: 0.8196 (mttt) cc_final: 0.7910 (mmmt) REVERT: A 739 MET cc_start: 0.7703 (mtp) cc_final: 0.7218 (ttt) REVERT: A 744 ASN cc_start: 0.8583 (t0) cc_final: 0.8248 (t0) REVERT: A 771 TYR cc_start: 0.8064 (p90) cc_final: 0.7607 (p90) REVERT: B 128 ARG cc_start: 0.6154 (mtt180) cc_final: 0.5818 (ptp-110) REVERT: B 243 TYR cc_start: 0.8631 (t80) cc_final: 0.8372 (t80) REVERT: B 441 ASP cc_start: 0.8742 (m-30) cc_final: 0.8324 (p0) REVERT: B 514 LEU cc_start: 0.8546 (pp) cc_final: 0.8271 (pp) REVERT: B 629 LEU cc_start: 0.7583 (mt) cc_final: 0.7374 (mt) REVERT: B 633 MET cc_start: 0.8818 (mtm) cc_final: 0.8273 (mtm) REVERT: B 759 MET cc_start: 0.7468 (mmt) cc_final: 0.6756 (mmp) REVERT: B 771 TYR cc_start: 0.7580 (p90) cc_final: 0.7215 (p90) outliers start: 3 outliers final: 0 residues processed: 182 average time/residue: 0.1340 time to fit residues: 34.9386 Evaluate side-chains 114 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 126 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.091660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067838 restraints weight = 68074.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.069450 restraints weight = 44831.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070546 restraints weight = 33284.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.071249 restraints weight = 26944.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071788 restraints weight = 23387.277| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13700 Z= 0.146 Angle : 0.671 22.123 18746 Z= 0.349 Chirality : 0.044 0.190 2122 Planarity : 0.005 0.056 2288 Dihedral : 17.724 88.440 2230 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % 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: -0.71 (0.20), residues: 1568 helix: 0.54 (0.19), residues: 715 sheet: -1.31 (0.32), residues: 197 loop : -1.26 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 656 TYR 0.022 0.002 TYR B 31 PHE 0.018 0.002 PHE A 372 TRP 0.018 0.002 TRP B 436 HIS 0.005 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (13700) covalent geometry : angle 0.67133 / 0.35 (18746) hydrogen bonds : bond 0.04817 / 3.24 ( 629) hydrogen bonds : angle 5.17028 / 3.57 ( 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 159 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.524 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: A 24 HIS cc_start: 0.7865 (p-80) cc_final: 0.7516 (p90) REVERT: A 239 CYS cc_start: 0.8678 (t) cc_final: 0.8329 (m) REVERT: A 365 LEU cc_start: 0.9516 (mt) cc_final: 0.9296 (mt) REVERT: A 508 GLU cc_start: 0.9488 (tt0) cc_final: 0.9214 (pt0) REVERT: A 574 ASP cc_start: 0.8591 (m-30) cc_final: 0.7719 (p0) REVERT: A 575 LYS cc_start: 0.8213 (mttt) cc_final: 0.7942 (mmmt) REVERT: A 771 TYR cc_start: 0.8190 (p90) cc_final: 0.7637 (p90) REVERT: B 88 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8770 (mm-30) REVERT: B 128 ARG cc_start: 0.5899 (mtt180) cc_final: 0.5675 (ptp-110) REVERT: B 243 TYR cc_start: 0.7960 (t80) cc_final: 0.7743 (t80) REVERT: B 432 GLU cc_start: 0.9205 (pm20) cc_final: 0.8847 (pm20) REVERT: B 441 ASP cc_start: 0.8642 (m-30) cc_final: 0.8267 (p0) REVERT: B 609 MET cc_start: 0.7875 (tpp) cc_final: 0.7587 (tpp) REVERT: B 629 LEU cc_start: 0.7732 (mt) cc_final: 0.7393 (mt) REVERT: B 633 MET cc_start: 0.8760 (mtm) cc_final: 0.8213 (mtm) REVERT: B 771 TYR cc_start: 0.7521 (p90) cc_final: 0.7133 (p90) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1192 time to fit residues: 28.0741 Evaluate side-chains 114 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 7.9990 chunk 146 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 156 optimal weight: 50.0000 chunk 26 optimal weight: 0.0010 chunk 49 optimal weight: 3.9990 overall best weight: 3.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 683 ASN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN B 526 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.085132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062007 restraints weight = 72476.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.063355 restraints weight = 49316.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.064257 restraints weight = 37776.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064932 restraints weight = 31442.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065203 restraints weight = 27511.827| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13700 Z= 0.237 Angle : 0.728 8.261 18746 Z= 0.379 Chirality : 0.045 0.229 2122 Planarity : 0.005 0.052 2288 Dihedral : 17.805 89.599 2230 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.42 % 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: -0.92 (0.20), residues: 1568 helix: 0.37 (0.18), residues: 730 sheet: -1.45 (0.31), residues: 200 loop : -1.40 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 274 TYR 0.019 0.002 TYR A 528 PHE 0.022 0.002 PHE B 155 TRP 0.007 0.001 TRP B 310 HIS 0.007 0.002 HIS B 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (13700) covalent geometry : angle 0.72834 / 0.38 (18746) hydrogen bonds : bond 0.04749 / 3.21 ( 629) hydrogen bonds : angle 5.29961 / 3.66 ( 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 144 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.470 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: A 239 CYS cc_start: 0.8636 (t) cc_final: 0.8281 (m) REVERT: A 372 PHE cc_start: 0.8595 (m-10) cc_final: 0.8325 (m-80) REVERT: A 445 ASP cc_start: 0.9373 (t0) cc_final: 0.8968 (p0) REVERT: A 508 GLU cc_start: 0.9571 (tt0) cc_final: 0.9349 (pt0) REVERT: A 574 ASP cc_start: 0.8590 (m-30) cc_final: 0.7747 (p0) REVERT: A 575 LYS cc_start: 0.8220 (mttt) cc_final: 0.7935 (mmmt) REVERT: A 617 MET cc_start: 0.8771 (mmp) cc_final: 0.8152 (tpt) REVERT: A 671 MET cc_start: 0.8568 (tpt) cc_final: 0.8240 (tpp) REVERT: A 759 MET cc_start: 0.8110 (mmm) cc_final: 0.7755 (mmm) REVERT: A 771 TYR cc_start: 0.8376 (p90) cc_final: 0.7739 (p90) REVERT: B 128 ARG cc_start: 0.6827 (mtt180) cc_final: 0.6067 (ptp-110) REVERT: B 155 PHE cc_start: 0.8667 (t80) cc_final: 0.8416 (t80) REVERT: B 609 MET cc_start: 0.8018 (tpp) cc_final: 0.7559 (tpp) REVERT: B 633 MET cc_start: 0.8736 (mtm) cc_final: 0.8162 (mtm) REVERT: B 717 ASN cc_start: 0.9015 (m-40) cc_final: 0.8757 (m-40) REVERT: B 759 MET cc_start: 0.7597 (mmt) cc_final: 0.7071 (mmp) REVERT: B 771 TYR cc_start: 0.8082 (p90) cc_final: 0.7454 (p90) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1244 time to fit residues: 26.4244 Evaluate side-chains 105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 763 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN B 746 HIS B 763 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.075909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055355 restraints weight = 85783.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.056910 restraints weight = 52713.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057958 restraints weight = 37205.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.058671 restraints weight = 28949.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.059152 restraints weight = 24261.840| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13700 Z= 0.147 Angle : 0.624 8.180 18746 Z= 0.328 Chirality : 0.043 0.198 2122 Planarity : 0.005 0.058 2288 Dihedral : 17.761 89.682 2230 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.08 % Allowed : 1.45 % Favored : 98.48 % 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: -0.56 (0.20), residues: 1568 helix: 0.73 (0.19), residues: 723 sheet: -1.22 (0.32), residues: 188 loop : -1.31 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 379 TYR 0.020 0.001 TYR A 528 PHE 0.018 0.001 PHE B 155 TRP 0.004 0.001 TRP A 137 HIS 0.006 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (13700) covalent geometry : angle 0.62446 / 0.33 (18746) hydrogen bonds : bond 0.04088 / 2.73 ( 629) hydrogen bonds : angle 4.98077 / 3.46 ( 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 146 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.513 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: A 239 CYS cc_start: 0.8645 (t) cc_final: 0.8222 (m) REVERT: A 368 MET cc_start: 0.8804 (ptp) cc_final: 0.8594 (ptp) REVERT: A 372 PHE cc_start: 0.8596 (m-10) cc_final: 0.8328 (m-80) REVERT: A 445 ASP cc_start: 0.9233 (t0) cc_final: 0.8850 (p0) REVERT: A 617 MET cc_start: 0.8724 (mmp) cc_final: 0.8459 (mmm) REVERT: A 671 MET cc_start: 0.8604 (tpt) cc_final: 0.8224 (tpp) REVERT: A 771 TYR cc_start: 0.8376 (p90) cc_final: 0.7719 (p90) REVERT: B 68 MET cc_start: 0.3987 (tmm) cc_final: 0.3721 (tmm) REVERT: B 128 ARG cc_start: 0.6455 (mtt180) cc_final: 0.5813 (ptp-110) REVERT: B 441 ASP cc_start: 0.8870 (m-30) cc_final: 0.8623 (m-30) REVERT: B 633 MET cc_start: 0.8916 (mtm) cc_final: 0.8300 (mtm) REVERT: B 717 ASN cc_start: 0.9026 (m-40) cc_final: 0.8739 (m-40) REVERT: B 759 MET cc_start: 0.7764 (mmt) cc_final: 0.7345 (mmp) REVERT: B 771 TYR cc_start: 0.7764 (p90) cc_final: 0.7198 (p90) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1312 time to fit residues: 27.9662 Evaluate side-chains 105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN B 78 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN B 616 ASN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.072087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052026 restraints weight = 87259.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053366 restraints weight = 55660.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.054271 restraints weight = 40347.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054907 restraints weight = 32002.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.055257 restraints weight = 27245.006| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 13700 Z= 0.309 Angle : 0.794 9.506 18746 Z= 0.407 Chirality : 0.047 0.294 2122 Planarity : 0.006 0.054 2288 Dihedral : 17.836 89.210 2230 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.87 % 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: -1.04 (0.20), residues: 1568 helix: 0.24 (0.18), residues: 728 sheet: -1.38 (0.32), residues: 200 loop : -1.46 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 492 TYR 0.025 0.002 TYR A 446 PHE 0.018 0.003 PHE B 155 TRP 0.008 0.002 TRP B 137 HIS 0.008 0.002 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.31 (13700) covalent geometry : angle 0.79415 / 0.41 (18746) hydrogen bonds : bond 0.05113 / 3.50 ( 629) hydrogen bonds : angle 5.39922 / 3.75 ( 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 133 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.516 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: A 239 CYS cc_start: 0.8776 (t) cc_final: 0.8408 (m) REVERT: A 372 PHE cc_start: 0.8613 (m-10) cc_final: 0.8371 (m-80) REVERT: A 445 ASP cc_start: 0.9317 (t0) cc_final: 0.8925 (p0) REVERT: A 617 MET cc_start: 0.8925 (mmp) cc_final: 0.8635 (mmm) REVERT: A 671 MET cc_start: 0.8793 (tpt) cc_final: 0.8451 (tpp) REVERT: A 744 ASN cc_start: 0.8828 (t0) cc_final: 0.8561 (p0) REVERT: A 759 MET cc_start: 0.8391 (mpp) cc_final: 0.8169 (mpp) REVERT: A 771 TYR cc_start: 0.8479 (p90) cc_final: 0.7969 (p90) REVERT: B 13 MET cc_start: 0.7003 (ppp) cc_final: 0.6630 (ppp) REVERT: B 68 MET cc_start: 0.4734 (tmm) cc_final: 0.4352 (tmm) REVERT: B 441 ASP cc_start: 0.8851 (m-30) cc_final: 0.8590 (m-30) REVERT: B 633 MET cc_start: 0.9014 (mtm) cc_final: 0.8389 (mtm) REVERT: B 759 MET cc_start: 0.7904 (mmp) cc_final: 0.7623 (mmp) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1244 time to fit residues: 24.4439 Evaluate side-chains 100 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.084125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060871 restraints weight = 72254.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062265 restraints weight = 48588.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.063196 restraints weight = 36846.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063858 restraints weight = 30576.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064281 restraints weight = 26786.701| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13700 Z= 0.183 Angle : 0.665 9.455 18746 Z= 0.348 Chirality : 0.044 0.222 2122 Planarity : 0.005 0.048 2288 Dihedral : 17.779 88.901 2230 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.70 (0.20), residues: 1568 helix: 0.60 (0.19), residues: 727 sheet: -1.21 (0.32), residues: 202 loop : -1.40 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 305 TYR 0.021 0.002 TYR A 446 PHE 0.019 0.002 PHE B 155 TRP 0.005 0.001 TRP A 436 HIS 0.005 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (13700) covalent geometry : angle 0.66451 / 0.35 (18746) hydrogen bonds : bond 0.04215 / 2.82 ( 629) hydrogen bonds : angle 5.11579 / 3.56 ( 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 129 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.526 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: A 313 MET cc_start: 0.7685 (tpp) cc_final: 0.7459 (tpt) REVERT: A 372 PHE cc_start: 0.8753 (m-10) cc_final: 0.8517 (m-80) REVERT: A 445 ASP cc_start: 0.9437 (t0) cc_final: 0.9024 (p0) REVERT: A 574 ASP cc_start: 0.8613 (m-30) cc_final: 0.7995 (p0) REVERT: A 617 MET cc_start: 0.8865 (mmp) cc_final: 0.8298 (tpt) REVERT: A 671 MET cc_start: 0.8658 (tpt) cc_final: 0.8289 (tpp) REVERT: A 744 ASN cc_start: 0.8781 (t0) cc_final: 0.8502 (p0) REVERT: A 771 TYR cc_start: 0.8380 (p90) cc_final: 0.7947 (p90) REVERT: B 13 MET cc_start: 0.7211 (ppp) cc_final: 0.6831 (ppp) REVERT: B 68 MET cc_start: 0.4836 (tmm) cc_final: 0.4515 (tmm) REVERT: B 441 ASP cc_start: 0.8757 (m-30) cc_final: 0.8492 (m-30) REVERT: B 633 MET cc_start: 0.8788 (mtm) cc_final: 0.8171 (mtm) REVERT: B 771 TYR cc_start: 0.7918 (p90) cc_final: 0.7677 (p90) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1291 time to fit residues: 24.5916 Evaluate side-chains 101 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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: 4.9990 chunk 146 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3753 r_free = 0.3753 target = 0.073134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053003 restraints weight = 85808.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054391 restraints weight = 54528.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055309 restraints weight = 39260.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055945 restraints weight = 31202.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.056401 restraints weight = 26421.133| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5227 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= 0.181 Angle : 0.656 7.687 18746 Z= 0.343 Chirality : 0.044 0.216 2122 Planarity : 0.005 0.049 2288 Dihedral : 17.770 89.681 2230 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -0.55 (0.20), residues: 1568 helix: 0.79 (0.19), residues: 727 sheet: -1.15 (0.33), residues: 199 loop : -1.42 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 305 TYR 0.020 0.002 TYR B 37 PHE 0.033 0.002 PHE B 36 TRP 0.007 0.001 TRP A 310 HIS 0.006 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (13700) covalent geometry : angle 0.65604 / 0.34 (18746) hydrogen bonds : bond 0.04158 / 2.82 ( 629) hydrogen bonds : angle 5.03465 / 3.50 ( 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 129 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.513 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: A 239 CYS cc_start: 0.8720 (t) cc_final: 0.8330 (m) REVERT: A 372 PHE cc_start: 0.8773 (m-10) cc_final: 0.8569 (m-80) REVERT: A 445 ASP cc_start: 0.9323 (t0) cc_final: 0.9092 (t0) REVERT: A 574 ASP cc_start: 0.8603 (m-30) cc_final: 0.7944 (p0) REVERT: A 617 MET cc_start: 0.8819 (mmp) cc_final: 0.8297 (tpt) REVERT: A 671 MET cc_start: 0.8753 (tpt) cc_final: 0.8362 (tpp) REVERT: A 744 ASN cc_start: 0.8806 (t0) cc_final: 0.8480 (p0) REVERT: A 759 MET cc_start: 0.8571 (mpp) cc_final: 0.8284 (mpp) REVERT: A 771 TYR cc_start: 0.8468 (p90) cc_final: 0.8032 (p90) REVERT: B 13 MET cc_start: 0.7015 (ppp) cc_final: 0.6729 (ppp) REVERT: B 397 MET cc_start: 0.9078 (mtm) cc_final: 0.8335 (mmm) REVERT: B 441 ASP cc_start: 0.8875 (m-30) cc_final: 0.8617 (m-30) REVERT: B 633 MET cc_start: 0.8958 (mtm) cc_final: 0.8332 (mtm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1289 time to fit residues: 24.4646 Evaluate side-chains 101 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.073716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.053315 restraints weight = 85550.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.054813 restraints weight = 52643.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.055828 restraints weight = 37143.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.056511 restraints weight = 28979.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056977 restraints weight = 24315.723| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13700 Z= 0.147 Angle : 0.640 11.748 18746 Z= 0.334 Chirality : 0.043 0.215 2122 Planarity : 0.006 0.151 2288 Dihedral : 17.742 89.561 2230 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.36 (0.21), residues: 1568 helix: 0.96 (0.19), residues: 727 sheet: -1.19 (0.32), residues: 215 loop : -1.29 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 608 TYR 0.018 0.002 TYR A 446 PHE 0.029 0.002 PHE B 36 TRP 0.008 0.001 TRP A 310 HIS 0.006 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (13700) covalent geometry : angle 0.63950 / 0.33 (18746) hydrogen bonds : bond 0.03850 / 2.59 ( 629) hydrogen bonds : angle 4.90509 / 3.41 ( 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 132 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.534 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: A 239 CYS cc_start: 0.8715 (t) cc_final: 0.8293 (m) REVERT: A 445 ASP cc_start: 0.9320 (t0) cc_final: 0.8861 (p0) REVERT: A 574 ASP cc_start: 0.8654 (m-30) cc_final: 0.7939 (p0) REVERT: A 617 MET cc_start: 0.8792 (mmp) cc_final: 0.8261 (tpt) REVERT: A 671 MET cc_start: 0.8692 (tpt) cc_final: 0.8296 (tpp) REVERT: A 742 VAL cc_start: 0.7550 (t) cc_final: 0.7333 (t) REVERT: A 759 MET cc_start: 0.8538 (mpp) cc_final: 0.8285 (mpp) REVERT: A 771 TYR cc_start: 0.8425 (p90) cc_final: 0.8040 (p90) REVERT: B 13 MET cc_start: 0.6863 (ppp) cc_final: 0.6593 (ppp) REVERT: B 397 MET cc_start: 0.8850 (mtm) cc_final: 0.8508 (mmm) REVERT: B 441 ASP cc_start: 0.8867 (m-30) cc_final: 0.8607 (m-30) REVERT: B 609 MET cc_start: 0.7855 (tpp) cc_final: 0.7410 (tpp) REVERT: B 633 MET cc_start: 0.8967 (mtm) cc_final: 0.8327 (mtm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1278 time to fit residues: 24.7128 Evaluate side-chains 107 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 116 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3761 r_free = 0.3761 target = 0.073362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053000 restraints weight = 85712.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.054418 restraints weight = 53102.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.055503 restraints weight = 37541.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.056151 restraints weight = 29362.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056612 restraints weight = 24738.767| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13700 Z= 0.159 Angle : 0.649 8.824 18746 Z= 0.338 Chirality : 0.043 0.216 2122 Planarity : 0.005 0.080 2288 Dihedral : 17.712 89.109 2230 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.31 (0.21), residues: 1568 helix: 1.00 (0.19), residues: 725 sheet: -1.08 (0.33), residues: 211 loop : -1.27 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 394 TYR 0.025 0.002 TYR B 31 PHE 0.026 0.002 PHE B 36 TRP 0.006 0.001 TRP A 310 HIS 0.006 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (13700) covalent geometry : angle 0.64920 / 0.34 (18746) hydrogen bonds : bond 0.03894 / 2.63 ( 629) hydrogen bonds : angle 4.88199 / 3.39 ( 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 131 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.533 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: A 239 CYS cc_start: 0.8707 (t) cc_final: 0.8283 (m) REVERT: A 445 ASP cc_start: 0.9343 (t0) cc_final: 0.8867 (p0) REVERT: A 574 ASP cc_start: 0.8668 (m-30) cc_final: 0.7924 (p0) REVERT: A 617 MET cc_start: 0.8748 (mmp) cc_final: 0.8251 (tpt) REVERT: A 671 MET cc_start: 0.8732 (tpt) cc_final: 0.8348 (tpp) REVERT: A 759 MET cc_start: 0.8553 (mpp) cc_final: 0.8258 (mpp) REVERT: A 771 TYR cc_start: 0.8364 (p90) cc_final: 0.7994 (p90) REVERT: B 441 ASP cc_start: 0.8877 (m-30) cc_final: 0.8614 (m-30) REVERT: B 609 MET cc_start: 0.7837 (tpp) cc_final: 0.7426 (tpp) REVERT: B 617 MET cc_start: 0.7772 (mmt) cc_final: 0.7484 (ttm) REVERT: B 633 MET cc_start: 0.8988 (mtm) cc_final: 0.8349 (mtm) REVERT: B 739 MET cc_start: 0.8904 (tmm) cc_final: 0.8665 (tmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1289 time to fit residues: 24.6869 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 : 0.486 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 0.0970 chunk 7 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3763 r_free = 0.3763 target = 0.073355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053027 restraints weight = 86254.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054481 restraints weight = 53108.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.055458 restraints weight = 37713.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056139 restraints weight = 29446.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056592 restraints weight = 24848.717| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5554 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= 0.153 Angle : 0.644 10.459 18746 Z= 0.334 Chirality : 0.043 0.217 2122 Planarity : 0.005 0.049 2288 Dihedral : 17.702 89.200 2230 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -0.30 (0.21), residues: 1568 helix: 0.98 (0.19), residues: 727 sheet: -1.04 (0.33), residues: 211 loop : -1.26 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 457 TYR 0.027 0.002 TYR B 31 PHE 0.025 0.002 PHE B 36 TRP 0.006 0.001 TRP B 709 HIS 0.006 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13700) covalent geometry : angle 0.64420 / 0.33 (18746) hydrogen bonds : bond 0.03786 / 2.55 ( 629) hydrogen bonds : angle 4.85994 / 3.37 ( 1714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.47 seconds wall clock time: 42 minutes 19.84 seconds (2539.84 seconds total)