Starting phenix.real_space_refine on Thu Jul 31 15:05:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ai5_11791/07_2025/7ai5_11791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai5_11791/07_2025/7ai5_11791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2025/7ai5_11791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2025/7ai5_11791.map" model { file = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2025/7ai5_11791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2025/7ai5_11791.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.84, per 1000 atoms: 0.66 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: 3.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.82 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: 5.86 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2168 1.30 - 1.44: 3618 1.44 - 1.58: 7714 1.58 - 1.72: 96 1.72 - 1.86: 104 Bond restraints: 13700 Sorted by residual: bond pdb=" C ILE A 650 " pdb=" O ILE A 650 " ideal model delta sigma weight residual 1.236 1.317 -0.080 1.04e-02 9.25e+03 5.99e+01 bond pdb=" C ILE A 636 " pdb=" O ILE A 636 " ideal model delta sigma weight residual 1.242 1.309 -0.067 1.13e-02 7.83e+03 3.55e+01 bond pdb=" C THR A 685 " pdb=" O THR A 685 " ideal model delta sigma weight residual 1.238 1.177 0.061 1.06e-02 8.90e+03 3.26e+01 bond pdb=" C PRO A 175 " pdb=" O PRO A 175 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.30e-02 5.92e+03 2.87e+01 bond pdb=" C GLY A 780 " pdb=" O GLY A 780 " ideal model delta sigma weight residual 1.232 1.283 -0.051 1.03e-02 9.43e+03 2.49e+01 ... (remaining 13695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 14597 2.29 - 4.57: 3849 4.57 - 6.86: 267 6.86 - 9.14: 24 9.14 - 11.43: 9 Bond angle restraints: 18746 Sorted by residual: angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 131.11 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" C PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta sigma weight residual 110.98 99.55 11.43 1.31e+00 5.83e-01 7.61e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 131.37 8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE A 155 " pdb=" CB PHE A 155 " pdb=" CG PHE A 155 " ideal model delta sigma weight residual 113.80 121.58 -7.78 1.00e+00 1.00e+00 6.05e+01 angle pdb=" N SER A 621 " pdb=" CA SER A 621 " pdb=" C SER A 621 " ideal model delta sigma weight residual 111.14 119.34 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 18741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7149 17.99 - 35.97: 713 35.97 - 53.96: 336 53.96 - 71.95: 78 71.95 - 89.93: 22 Dihedral angle restraints: 8298 sinusoidal: 3722 harmonic: 4576 Sorted by residual: dihedral pdb=" C THR A 273 " pdb=" N THR A 273 " pdb=" CA THR A 273 " pdb=" CB THR A 273 " ideal model delta harmonic sigma weight residual -122.00 -109.90 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO A 615 " pdb=" N PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta harmonic sigma weight residual -120.70 -108.69 -12.01 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C ASN B 593 " pdb=" N ASN B 593 " pdb=" CA ASN B 593 " pdb=" CB ASN B 593 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 8295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1228 0.088 - 0.177: 731 0.177 - 0.265: 139 0.265 - 0.353: 21 0.353 - 0.442: 3 Chirality restraints: 2122 Sorted by residual: chirality pdb=" CB VAL A 640 " pdb=" CA VAL A 640 " pdb=" CG1 VAL A 640 " pdb=" CG2 VAL A 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ALA A 766 " pdb=" N ALA A 766 " pdb=" C ALA A 766 " pdb=" CB ALA A 766 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA VAL B 657 " pdb=" N VAL B 657 " pdb=" C VAL B 657 " pdb=" CB VAL B 657 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2119 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 635 " 0.021 2.00e-02 2.50e+03 3.60e-02 2.59e+01 pdb=" CG TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 635 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 635 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 635 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 635 " 0.041 2.00e-02 2.50e+03 pdb=" OH TYR A 635 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 132 " 0.022 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU A 132 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU A 132 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A 133 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 309 " -0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ARG A 309 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG A 309 " -0.027 2.00e-02 2.50e+03 pdb=" N TRP A 310 " -0.025 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 5547 2.96 - 3.44: 13307 3.44 - 3.93: 22952 3.93 - 4.41: 26036 4.41 - 4.90: 40766 Nonbonded interactions: 108608 Sorted by model distance: nonbonded pdb=" N ASN B 616 " pdb=" O ASN B 616 " model vdw 2.472 2.496 nonbonded pdb=" OD1 ASP B 296 " pdb=" OG1 THR B 298 " model vdw 2.479 3.040 nonbonded pdb=" O ASP B 98 " pdb=" OG1 THR B 101 " model vdw 2.484 3.040 nonbonded pdb=" N GLU A 731 " pdb=" OE1 GLU A 731 " model vdw 2.511 3.120 nonbonded pdb=" N TYR A 702 " pdb=" N ASP A 703 " model vdw 2.521 2.560 ... (remaining 108603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.450 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.080 13700 Z= 1.031 Angle : 1.846 11.431 18746 Z= 1.375 Chirality : 0.104 0.442 2122 Planarity : 0.008 0.054 2288 Dihedral : 18.260 89.933 5346 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.14 % Allowed : 9.60 % Favored : 89.25 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (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 TRP 0.022 0.005 TRP A 310 HIS 0.040 0.006 HIS A 728 PHE 0.070 0.006 PHE A 36 TYR 0.072 0.007 TYR A 635 ARG 0.032 0.002 ARG A 652 Details of bonding type rmsd hydrogen bonds : bond 0.22752 ( 629) hydrogen bonds : angle 8.08747 ( 1714) covalent geometry : bond 0.01388 (13700) covalent geometry : angle 1.84595 (18746) *********************** 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 : 1.483 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: 0.9282 (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: 0.8247 (mmt) REVERT: A 686 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8191 (tp30) REVERT: A 730 PHE cc_start: 0.8007 (t80) cc_final: 0.7600 (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: 0.9137 (tt0) REVERT: B 173 THR cc_start: 0.8876 (p) cc_final: 0.8181 (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: 0.8558 (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: 0.8270 (mtm) REVERT: B 703 ASP cc_start: 0.8564 (t70) cc_final: 0.7946 (t70) REVERT: B 730 PHE cc_start: 0.7229 (t80) cc_final: 0.6938 (t80) REVERT: B 732 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8237 (mt) outliers start: 15 outliers final: 3 residues processed: 300 average time/residue: 0.3374 time to fit residues: 137.0171 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 : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 683 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 683 ASN ** B 763 GLN ** 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 = 0.3859 r_free = 0.3859 target = 0.078315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.057832 restraints weight = 84202.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.059605 restraints weight = 50047.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.060787 restraints weight = 34132.970| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3291 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= 0.180 Angle : 0.693 8.557 18746 Z= 0.371 Chirality : 0.044 0.230 2122 Planarity : 0.005 0.087 2288 Dihedral : 18.308 89.378 2292 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.23 % Allowed : 2.74 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1568 helix: 0.50 (0.19), residues: 725 sheet: -1.55 (0.31), residues: 189 loop : -1.36 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 137 HIS 0.006 0.001 HIS B 370 PHE 0.024 0.002 PHE A 372 TYR 0.018 0.002 TYR A 528 ARG 0.010 0.001 ARG B 579 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 629) hydrogen bonds : angle 5.31110 ( 1714) covalent geometry : bond 0.00388 (13700) covalent geometry : angle 0.69256 (18746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 1.533 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 CYS cc_start: 0.8726 (t) cc_final: 0.8174 (m) REVERT: A 508 GLU cc_start: 0.9377 (tt0) cc_final: 0.9152 (pt0) REVERT: A 574 ASP cc_start: 0.8575 (m-30) cc_final: 0.7769 (p0) REVERT: A 575 LYS cc_start: 0.8262 (mttt) cc_final: 0.7971 (mmmt) REVERT: A 744 ASN cc_start: 0.8680 (t0) cc_final: 0.8475 (t0) REVERT: A 771 TYR cc_start: 0.8175 (p90) cc_final: 0.7631 (p90) REVERT: B 243 TYR cc_start: 0.8522 (t80) cc_final: 0.7959 (t80) REVERT: B 441 ASP cc_start: 0.8742 (m-30) cc_final: 0.8346 (p0) REVERT: B 629 LEU cc_start: 0.7728 (mt) cc_final: 0.7289 (mt) REVERT: B 633 MET cc_start: 0.8771 (mtm) cc_final: 0.8411 (mtm) REVERT: B 771 TYR cc_start: 0.7651 (p90) cc_final: 0.7327 (p90) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 0.2982 time to fit residues: 74.8444 Evaluate side-chains 118 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 82 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 17 optimal weight: 0.0040 chunk 153 optimal weight: 1.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 763 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN B 746 HIS ** 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 = 0.3824 r_free = 0.3824 target = 0.076628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.056151 restraints weight = 84952.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.057737 restraints weight = 51971.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.058760 restraints weight = 36423.135| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13700 Z= 0.168 Angle : 0.625 6.689 18746 Z= 0.333 Chirality : 0.042 0.240 2122 Planarity : 0.005 0.055 2288 Dihedral : 18.367 89.763 2292 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1568 helix: 0.71 (0.19), residues: 734 sheet: -1.18 (0.31), residues: 201 loop : -1.24 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS B 24 PHE 0.020 0.002 PHE A 372 TYR 0.018 0.001 TYR A 528 ARG 0.019 0.001 ARG B 656 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 629) hydrogen bonds : angle 5.03248 ( 1714) covalent geometry : bond 0.00369 (13700) covalent geometry : angle 0.62504 (18746) *********************** 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 153 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.381 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: A 239 CYS cc_start: 0.8721 (t) cc_final: 0.8245 (m) REVERT: A 372 PHE cc_start: 0.8602 (m-80) cc_final: 0.8388 (m-80) REVERT: A 445 ASP cc_start: 0.9239 (t0) cc_final: 0.8880 (p0) REVERT: A 617 MET cc_start: 0.8767 (mmp) cc_final: 0.8527 (mmm) REVERT: A 744 ASN cc_start: 0.8678 (t0) cc_final: 0.8396 (t0) REVERT: A 771 TYR cc_start: 0.8324 (p90) cc_final: 0.7625 (p90) REVERT: B 128 ARG cc_start: 0.6344 (mtt180) cc_final: 0.6008 (mtp85) REVERT: B 609 MET cc_start: 0.8067 (tpp) cc_final: 0.7741 (tpp) REVERT: B 633 MET cc_start: 0.8873 (mtm) cc_final: 0.8424 (mtm) REVERT: B 717 ASN cc_start: 0.8964 (m-40) cc_final: 0.8682 (m-40) REVERT: B 759 MET cc_start: 0.7543 (mmt) cc_final: 0.6923 (mmp) REVERT: B 771 TYR cc_start: 0.7741 (p90) cc_final: 0.7407 (p90) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.2680 time to fit residues: 59.3527 Evaluate side-chains 109 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** B 370 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 = 0.3801 r_free = 0.3801 target = 0.075307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054764 restraints weight = 85023.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.056346 restraints weight = 52352.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.057406 restraints weight = 36866.057| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13700 Z= 0.172 Angle : 0.623 7.264 18746 Z= 0.330 Chirality : 0.042 0.191 2122 Planarity : 0.005 0.048 2288 Dihedral : 18.311 89.930 2292 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1568 helix: 0.88 (0.19), residues: 731 sheet: -1.21 (0.31), residues: 193 loop : -1.19 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 709 HIS 0.005 0.001 HIS B 24 PHE 0.021 0.002 PHE B 155 TYR 0.020 0.002 TYR B 509 ARG 0.005 0.001 ARG A 788 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 629) hydrogen bonds : angle 4.92947 ( 1714) covalent geometry : bond 0.00373 (13700) covalent geometry : angle 0.62349 (18746) *********************** 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 142 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.362 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 239 CYS cc_start: 0.8681 (t) cc_final: 0.8251 (m) REVERT: A 372 PHE cc_start: 0.8646 (m-80) cc_final: 0.8401 (m-80) REVERT: A 445 ASP cc_start: 0.9245 (t0) cc_final: 0.8852 (p0) REVERT: A 617 MET cc_start: 0.8836 (mmp) cc_final: 0.8311 (mmt) REVERT: A 744 ASN cc_start: 0.8707 (t0) cc_final: 0.8408 (t0) REVERT: A 771 TYR cc_start: 0.8337 (p90) cc_final: 0.7589 (p90) REVERT: B 13 MET cc_start: 0.6739 (ppp) cc_final: 0.6517 (ppp) REVERT: B 441 ASP cc_start: 0.8870 (m-30) cc_final: 0.8617 (m-30) REVERT: B 633 MET cc_start: 0.8928 (mtm) cc_final: 0.8465 (mtm) REVERT: B 717 ASN cc_start: 0.9014 (m-40) cc_final: 0.8708 (m-40) REVERT: B 759 MET cc_start: 0.7884 (mmt) cc_final: 0.7517 (mmp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2639 time to fit residues: 54.3131 Evaluate side-chains 108 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.074030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053573 restraints weight = 85942.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.055085 restraints weight = 52925.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.056123 restraints weight = 37348.417| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13700 Z= 0.176 Angle : 0.635 8.536 18746 Z= 0.333 Chirality : 0.042 0.170 2122 Planarity : 0.005 0.062 2288 Dihedral : 18.326 89.146 2292 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1568 helix: 0.96 (0.19), residues: 731 sheet: -1.16 (0.32), residues: 210 loop : -1.15 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS B 24 PHE 0.021 0.002 PHE B 36 TYR 0.017 0.002 TYR B 509 ARG 0.012 0.001 ARG B 697 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 629) hydrogen bonds : angle 4.97700 ( 1714) covalent geometry : bond 0.00380 (13700) covalent geometry : angle 0.63458 (18746) *********************** 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 133 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.510 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 51 LEU cc_start: 0.8953 (tp) cc_final: 0.8652 (tp) REVERT: A 306 MET cc_start: 0.9236 (tpt) cc_final: 0.8975 (tpp) REVERT: A 372 PHE cc_start: 0.8579 (m-10) cc_final: 0.8301 (m-80) REVERT: A 445 ASP cc_start: 0.9226 (t0) cc_final: 0.9018 (t0) REVERT: A 574 ASP cc_start: 0.8571 (m-30) cc_final: 0.8001 (p0) REVERT: A 617 MET cc_start: 0.8806 (mmp) cc_final: 0.8380 (tpt) REVERT: B 441 ASP cc_start: 0.8831 (m-30) cc_final: 0.8572 (m-30) REVERT: B 609 MET cc_start: 0.7635 (tpp) cc_final: 0.7333 (tpp) REVERT: B 633 MET cc_start: 0.8872 (mtm) cc_final: 0.8577 (mtm) REVERT: B 671 MET cc_start: 0.8134 (ptt) cc_final: 0.6981 (tpp) REVERT: B 717 ASN cc_start: 0.8991 (m-40) cc_final: 0.8693 (m-40) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2783 time to fit residues: 53.7559 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 : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.075745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.055155 restraints weight = 85912.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056750 restraints weight = 52665.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.057836 restraints weight = 36913.401| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13700 Z= 0.116 Angle : 0.573 11.064 18746 Z= 0.301 Chirality : 0.041 0.243 2122 Planarity : 0.004 0.052 2288 Dihedral : 18.211 89.991 2292 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1568 helix: 1.28 (0.19), residues: 730 sheet: -1.04 (0.32), residues: 202 loop : -1.12 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 709 HIS 0.004 0.001 HIS B 24 PHE 0.018 0.001 PHE B 36 TYR 0.021 0.001 TYR A 446 ARG 0.006 0.000 ARG B 697 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 629) hydrogen bonds : angle 4.68435 ( 1714) covalent geometry : bond 0.00250 (13700) covalent geometry : angle 0.57271 (18746) *********************** 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 140 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.561 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 51 LEU cc_start: 0.8995 (tp) cc_final: 0.8652 (tp) REVERT: A 239 CYS cc_start: 0.8635 (t) cc_final: 0.8223 (m) REVERT: A 372 PHE cc_start: 0.8738 (m-10) cc_final: 0.8413 (m-80) REVERT: A 445 ASP cc_start: 0.9331 (t0) cc_final: 0.9126 (t0) REVERT: A 574 ASP cc_start: 0.8709 (m-30) cc_final: 0.8014 (p0) REVERT: A 617 MET cc_start: 0.8681 (mmp) cc_final: 0.8201 (tpt) REVERT: A 692 MET cc_start: 0.7417 (mmp) cc_final: 0.7087 (mmm) REVERT: A 771 TYR cc_start: 0.8266 (p90) cc_final: 0.8011 (p90) REVERT: B 306 MET cc_start: 0.9123 (tpt) cc_final: 0.8895 (tpt) REVERT: B 397 MET cc_start: 0.9065 (mtm) cc_final: 0.8277 (mmm) REVERT: B 441 ASP cc_start: 0.8845 (m-30) cc_final: 0.8584 (m-30) REVERT: B 609 MET cc_start: 0.7506 (tpp) cc_final: 0.7258 (tpp) REVERT: B 633 MET cc_start: 0.8933 (mtm) cc_final: 0.8571 (mtm) REVERT: B 671 MET cc_start: 0.7931 (ptt) cc_final: 0.6936 (tpp) REVERT: B 717 ASN cc_start: 0.9131 (m-40) cc_final: 0.8793 (m-40) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2900 time to fit residues: 58.3530 Evaluate side-chains 111 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053308 restraints weight = 86345.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054827 restraints weight = 53556.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.055848 restraints weight = 37783.992| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13700 Z= 0.178 Angle : 0.640 14.892 18746 Z= 0.333 Chirality : 0.042 0.228 2122 Planarity : 0.005 0.049 2288 Dihedral : 18.197 88.917 2292 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1568 helix: 1.07 (0.19), residues: 731 sheet: -0.96 (0.33), residues: 196 loop : -1.18 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 709 HIS 0.005 0.001 HIS B 24 PHE 0.017 0.002 PHE B 36 TYR 0.020 0.002 TYR A 446 ARG 0.007 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 629) hydrogen bonds : angle 4.96425 ( 1714) covalent geometry : bond 0.00382 (13700) covalent geometry : angle 0.63981 (18746) *********************** 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 134 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.513 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: A 51 LEU cc_start: 0.9049 (tp) cc_final: 0.8722 (tp) REVERT: A 239 CYS cc_start: 0.8667 (t) cc_final: 0.8302 (m) REVERT: A 372 PHE cc_start: 0.8718 (m-10) cc_final: 0.8479 (m-80) REVERT: A 445 ASP cc_start: 0.9374 (t0) cc_final: 0.9166 (t0) REVERT: A 574 ASP cc_start: 0.8742 (m-30) cc_final: 0.8004 (p0) REVERT: A 617 MET cc_start: 0.8785 (mmp) cc_final: 0.8328 (tpt) REVERT: A 759 MET cc_start: 0.8535 (mpp) cc_final: 0.8200 (mpp) REVERT: A 771 TYR cc_start: 0.8303 (p90) cc_final: 0.8064 (p90) REVERT: B 397 MET cc_start: 0.8864 (mtm) cc_final: 0.8650 (mmm) REVERT: B 441 ASP cc_start: 0.8832 (m-30) cc_final: 0.8567 (m-30) REVERT: B 609 MET cc_start: 0.7607 (tpp) cc_final: 0.7307 (tpp) REVERT: B 633 MET cc_start: 0.8976 (mtm) cc_final: 0.8625 (mtm) REVERT: B 671 MET cc_start: 0.8007 (ptt) cc_final: 0.6927 (tpp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2782 time to fit residues: 54.3431 Evaluate side-chains 98 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 99 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.074194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.053794 restraints weight = 86013.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.055351 restraints weight = 52669.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056372 restraints weight = 36915.858| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13700 Z= 0.141 Angle : 0.627 10.838 18746 Z= 0.324 Chirality : 0.042 0.207 2122 Planarity : 0.005 0.049 2288 Dihedral : 18.176 89.941 2292 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1568 helix: 1.19 (0.19), residues: 732 sheet: -0.90 (0.34), residues: 196 loop : -1.15 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 709 HIS 0.006 0.001 HIS B 24 PHE 0.014 0.001 PHE B 36 TYR 0.018 0.001 TYR A 446 ARG 0.007 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 629) hydrogen bonds : angle 4.83083 ( 1714) covalent geometry : bond 0.00310 (13700) covalent geometry : angle 0.62733 (18746) *********************** 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 128 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9051 (tp) cc_final: 0.8725 (tp) REVERT: A 239 CYS cc_start: 0.8618 (t) cc_final: 0.8243 (m) REVERT: A 306 MET cc_start: 0.9275 (tpt) cc_final: 0.8746 (tpp) REVERT: A 368 MET cc_start: 0.9078 (ptt) cc_final: 0.8854 (ptp) REVERT: A 372 PHE cc_start: 0.8775 (m-10) cc_final: 0.8531 (m-80) REVERT: A 445 ASP cc_start: 0.9379 (t0) cc_final: 0.9164 (t0) REVERT: A 574 ASP cc_start: 0.8774 (m-30) cc_final: 0.7977 (p0) REVERT: A 617 MET cc_start: 0.8792 (mmp) cc_final: 0.8238 (tpt) REVERT: A 742 VAL cc_start: 0.7460 (t) cc_final: 0.7212 (t) REVERT: A 759 MET cc_start: 0.8494 (mpp) cc_final: 0.8194 (mpp) REVERT: B 302 MET cc_start: 0.8539 (mpp) cc_final: 0.8099 (mpp) REVERT: B 441 ASP cc_start: 0.8836 (m-30) cc_final: 0.8565 (m-30) REVERT: B 609 MET cc_start: 0.7543 (tpp) cc_final: 0.7228 (tpp) REVERT: B 633 MET cc_start: 0.9002 (mtm) cc_final: 0.8352 (mtm) REVERT: B 671 MET cc_start: 0.8002 (ptt) cc_final: 0.7002 (tpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2534 time to fit residues: 48.4468 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 : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.073862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.053551 restraints weight = 85423.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054993 restraints weight = 52920.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055987 restraints weight = 37701.294| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13700 Z= 0.142 Angle : 0.616 8.050 18746 Z= 0.319 Chirality : 0.041 0.200 2122 Planarity : 0.005 0.049 2288 Dihedral : 18.142 89.905 2292 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1568 helix: 1.16 (0.19), residues: 730 sheet: -0.90 (0.35), residues: 185 loop : -1.08 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 709 HIS 0.006 0.001 HIS B 24 PHE 0.013 0.001 PHE B 36 TYR 0.018 0.001 TYR A 446 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 629) hydrogen bonds : angle 4.80208 ( 1714) covalent geometry : bond 0.00313 (13700) covalent geometry : angle 0.61567 (18746) *********************** 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 127 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9040 (tp) cc_final: 0.8718 (tp) REVERT: A 239 CYS cc_start: 0.8673 (t) cc_final: 0.8274 (m) REVERT: A 269 MET cc_start: 0.7294 (tpp) cc_final: 0.6971 (mmt) REVERT: A 368 MET cc_start: 0.9066 (ptt) cc_final: 0.8808 (ptp) REVERT: A 372 PHE cc_start: 0.8826 (m-10) cc_final: 0.8570 (m-80) REVERT: A 445 ASP cc_start: 0.9428 (t0) cc_final: 0.9193 (t0) REVERT: A 574 ASP cc_start: 0.8826 (m-30) cc_final: 0.7987 (p0) REVERT: A 617 MET cc_start: 0.8775 (mmp) cc_final: 0.8199 (tpt) REVERT: A 692 MET cc_start: 0.7217 (mmp) cc_final: 0.7014 (mmm) REVERT: A 759 MET cc_start: 0.8531 (mpp) cc_final: 0.8053 (mpp) REVERT: B 441 ASP cc_start: 0.8849 (m-30) cc_final: 0.8579 (m-30) REVERT: B 633 MET cc_start: 0.9017 (mtm) cc_final: 0.8358 (mtm) REVERT: B 671 MET cc_start: 0.7977 (ptt) cc_final: 0.7033 (tpp) REVERT: B 739 MET cc_start: 0.8915 (tmm) cc_final: 0.8652 (tmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2654 time to fit residues: 49.1761 Evaluate side-chains 100 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.0870 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.072928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052626 restraints weight = 86633.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054014 restraints weight = 53523.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054970 restraints weight = 38325.657| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13700 Z= 0.160 Angle : 0.637 8.680 18746 Z= 0.331 Chirality : 0.042 0.216 2122 Planarity : 0.005 0.048 2288 Dihedral : 18.139 89.847 2292 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1568 helix: 1.08 (0.19), residues: 729 sheet: -0.70 (0.35), residues: 190 loop : -1.05 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.006 0.001 HIS B 24 PHE 0.021 0.002 PHE B 155 TYR 0.018 0.002 TYR B 509 ARG 0.011 0.001 ARG A 788 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 629) hydrogen bonds : angle 4.88200 ( 1714) covalent geometry : bond 0.00350 (13700) covalent geometry : angle 0.63736 (18746) ********************** 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 124 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8969 (tp) cc_final: 0.8630 (tp) REVERT: A 239 CYS cc_start: 0.8527 (t) cc_final: 0.8237 (m) REVERT: A 368 MET cc_start: 0.8923 (ptt) cc_final: 0.8708 (ptp) REVERT: A 372 PHE cc_start: 0.8681 (m-10) cc_final: 0.8459 (m-80) REVERT: A 445 ASP cc_start: 0.9437 (t0) cc_final: 0.8906 (p0) REVERT: A 574 ASP cc_start: 0.8717 (m-30) cc_final: 0.7870 (p0) REVERT: A 617 MET cc_start: 0.8791 (mmp) cc_final: 0.8283 (tpt) REVERT: A 759 MET cc_start: 0.8705 (mpp) cc_final: 0.8332 (mpp) REVERT: B 113 ILE cc_start: 0.8508 (mp) cc_final: 0.8261 (mp) REVERT: B 241 LEU cc_start: 0.9668 (mt) cc_final: 0.9302 (tp) REVERT: B 441 ASP cc_start: 0.8834 (m-30) cc_final: 0.8547 (m-30) REVERT: B 633 MET cc_start: 0.8963 (mtm) cc_final: 0.8332 (mtm) REVERT: B 671 MET cc_start: 0.7964 (ptt) cc_final: 0.7036 (tpp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2568 time to fit residues: 47.6726 Evaluate side-chains 96 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 58 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 370 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.074888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054490 restraints weight = 85717.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055982 restraints weight = 53345.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056983 restraints weight = 37957.253| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13700 Z= 0.112 Angle : 0.597 8.611 18746 Z= 0.308 Chirality : 0.041 0.195 2122 Planarity : 0.004 0.052 2288 Dihedral : 18.040 89.760 2292 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1568 helix: 1.26 (0.19), residues: 730 sheet: -0.64 (0.34), residues: 207 loop : -0.93 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 709 HIS 0.003 0.001 HIS A 760 PHE 0.020 0.001 PHE A 143 TYR 0.019 0.001 TYR A 528 ARG 0.007 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 629) hydrogen bonds : angle 4.67854 ( 1714) covalent geometry : bond 0.00241 (13700) covalent geometry : angle 0.59732 (18746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4379.43 seconds wall clock time: 76 minutes 38.57 seconds (4598.57 seconds total)